From 2d8b3e82bba04ee8fff0d1d05d7bb8cff38f5c2f Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 2 Feb 2018 16:31:34 +0100
Subject: [PATCH] kinetics equation can contain compartment id
---
.../CellDesignerElementCollection.java | 6 +-
.../alias/CompartmentAliasXmlParser.java | 317 ++++-----
.../alias/ComplexAliasXmlParser.java | 1 +
.../alias/SpeciesAliasXmlParser.java | 442 ++++++------
.../reaction/ReactionFromXml.java | 26 +-
.../reaction/ReactionXmlParser.java | 6 +-
.../structure/CellDesignerElement.java | 6 +-
.../alias/AliasCollectionXmlParserTest.java | 641 +++++++++---------
.../alias/CompartmentAliasXmlParserTest.java | 461 +++++++------
.../alias/ComplexAliasXmlParserTest.java | 119 ++--
.../alias/SpeciesAliasXmlParserTest.java | 594 ++++++++--------
.../reaction/ReactionFromXmlTest.java | 18 +-
.../reaction/ReactionParserTests.java | 12 +
.../reactions/kinetics_with_compartment.xml | 189 ++++++
.../mapviewer/model/map/species/Element.java | 2 +-
15 files changed, 1558 insertions(+), 1282 deletions(-)
create mode 100644 converter-CellDesigner/testFiles/reactions/kinetics_with_compartment.xml
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
index 1eb8a39ac4..6857681265 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerElementCollection.java
@@ -155,7 +155,7 @@ public class CellDesignerElementCollection {
}
}
- // identifier that distinguish elements in sbml depends only on type,
+ // identifier that distinguish elements in SBML depends only on type,
// name, compartment, modifications, homodimer, state, complex where it's
// located,
// children of the complex
@@ -216,7 +216,7 @@ public class CellDesignerElementCollection {
* @param id
* id that should be used for identifying element
*/
- private void addElement(CellDesignerElement<?> element, String id) {
+ public void addElement(CellDesignerElement<?> element, String id) {
if (elementById.get(id) != null) {
throw new InvalidArgumentException(
"[" + element.getClass().getSimpleName() + " " + element.getElementId() + "]\t" + "Element with given id alread exists. ID: " + id);
@@ -233,7 +233,7 @@ public class CellDesignerElementCollection {
* @param element
* element to be added
*/
- public void addModelElement(Species modelElement, CellDesignerElement<?> element) {
+ public void addModelElement(Element modelElement, CellDesignerElement<?> element) {
addElement(element, getElementId(modelElement));
if (getElementByElementId(element.getElementId()) == null) {
addElement(element);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
index f3a8bf8492..bb923a34ce 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParser.java
@@ -26,162 +26,165 @@ import lcsb.mapviewer.model.map.model.Model;
*/
public class CompartmentAliasXmlParser extends AbstractAliasXmlParser<Compartment> {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class.getName());
-
- /**
- * Model for which we are parsing aliases.
- */
- private Model model = null;
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- * @param model
- * model for which this parser will be used
- */
- public CompartmentAliasXmlParser(CellDesignerElementCollection elements, Model model) {
- this.model = model;
- this.elements = elements;
- }
-
- @Override
- Compartment parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
-
- String compartmentId = getNodeAttr("compartment", aliasNode);
- CellDesignerCompartment compartment = elements.getElementByElementId(compartmentId);
- if (compartment == null) {
- throw new InvalidXmlSchemaException("Compartment does not exist in a model: " + compartmentId);
- }
- String aliasId = getNodeAttr("id", aliasNode);
- Compartment result = compartment.createModelElement(aliasId);
-
- NodeList nodes = aliasNode.getChildNodes();
- for (int i = 0; i < nodes.getLength(); i++) {
- Node node = nodes.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
- String type = getNodeValue(node);
- if (type.equalsIgnoreCase("SQUARE")) {
- result = new SquareCompartment(result);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_NORTH")) {
- result = new BottomSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_SOUTH")) {
- result = new TopSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_WEST")) {
- result = new RightSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_EAST")) {
- result = new LeftSquareCompartment(result, model);
- } else if (type.equalsIgnoreCase("OVAL")) {
- result = new OvalCompartment(result);
- } else {
- throw new InvalidXmlSchemaException("Unknown compartment type: " + type);
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("x", node));
- result.setY(getNodeAttr("y", node));
- result.setWidth(getNodeAttr("w", node));
- result.setHeight(getNodeAttr("h", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:doubleLine")) {
- result.setLineThickness(getNodeAttr("thickness", node));
- result.setLineOuterWidth(getNodeAttr("outerWidth", node));
- result.setLineInnerWidth(getNodeAttr("innerWidth", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
- result.setColor(getCommonParser().getColor(node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
- // not handled
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:point")) {
- if (result instanceof BottomSquareCompartment) {
- result.setY(getNodeAttr("y", node));
- } else if (result instanceof LeftSquareCompartment) {
- result.setX(getNodeAttr("x", node));
- } else if (result instanceof RightSquareCompartment) {
- result.setX(getNodeAttr("x", node));
- result.setWidth(result.getWidth() - result.getX());
- } else if (result instanceof TopSquareCompartment) {
- result.setY(getNodeAttr("y", node));
- } else {
- throw new InvalidXmlSchemaException("Don't know what to do with celldesigner:point for class: " + result.getClass());
- }
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:namePoint")) {
- result.setNamePoint(getCommonParser().getPosition(node));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:compartmentAlias: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- @Override
- public String toXml(Compartment compartment) {
- StringBuilder sb = new StringBuilder("");
-
- sb.append("<celldesigner:compartmentAlias ");
- sb.append("id=\"" + compartment.getElementId() + "\" ");
- sb.append("compartment=\"" + elements.getElementId(compartment) + "\">\n");
-
- boolean bounds = true;
-
- if (compartment.getClass().getName().equals(SquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE</celldesigner:class>\n");
- } else if (compartment.getClass().getName().equals(OvalCompartment.class.getName())) {
- sb.append("<celldesigner:class>OVAL</celldesigner:class>\n");
- } else if (compartment.getClass().getName().equals(BottomSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_NORTH</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
- } else if (compartment.getClass().getName().equals(TopSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_SOUTH</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
- } else if (compartment.getClass().getName().equals(LeftSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_EAST</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"" + compartment.getWidth() + "\" y=\"10\"/>");
- } else if (compartment.getClass().getName().equals(RightSquareCompartment.class.getName())) {
- sb.append("<celldesigner:class>SQUARE_CLOSEUP_WEST</celldesigner:class>\n");
- bounds = false;
- sb.append("<celldesigner:point x=\"" + compartment.getX() + "\" y=\"10\"/>");
- } else {
- throw new NotImplementedException("Unknown compartment class: " + compartment.getClass());
- }
- if (bounds) {
- sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + compartment.getX() + "\" ");
- sb.append("y=\"" + compartment.getY() + "\" ");
- sb.append("w=\"" + compartment.getWidth() + "\" ");
- sb.append("h=\"" + compartment.getHeight() + "\"/>\n");
- }
-
- sb.append("<celldesigner:namePoint ");
- sb.append("x=\"" + compartment.getNamePoint().getX() + "\" ");
- sb.append("y=\"" + compartment.getNamePoint().getY() + "\"/>\n");
-
- sb.append("<celldesigner:doubleLine ");
- sb.append("thickness=\"" + compartment.getThickness() + "\" ");
- sb.append("outerWidth=\"" + compartment.getOuterWidth() + "\" ");
- sb.append("innerWidth=\"" + compartment.getInnerWidth() + "\"/>\n");
-
- sb.append("<celldesigner:paint ");
- sb.append("color=\"" + colorToString(compartment.getColor()) + "\" scheme=\"Color\"/>\n");
-
- sb.append("</celldesigner:compartmentAlias>\n");
-
- return sb.toString();
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class.getName());
+
+ /**
+ * Model for which we are parsing aliases.
+ */
+ private Model model = null;
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Default constructor.
+ *
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ * @param model
+ * model for which this parser will be used
+ */
+ public CompartmentAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.model = model;
+ this.elements = elements;
+ }
+
+ @Override
+ Compartment parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+
+ String compartmentId = getNodeAttr("compartment", aliasNode);
+ CellDesignerCompartment compartment = elements.getElementByElementId(compartmentId);
+ if (compartment == null) {
+ throw new InvalidXmlSchemaException("Compartment does not exist in a model: " + compartmentId);
+ }
+ String aliasId = getNodeAttr("id", aliasNode);
+ Compartment result = compartment.createModelElement(aliasId);
+ elements.addElement(compartment, aliasId);
+
+ NodeList nodes = aliasNode.getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++) {
+ Node node = nodes.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:class")) {
+ String type = getNodeValue(node);
+ if (type.equalsIgnoreCase("SQUARE")) {
+ result = new SquareCompartment(result);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_NORTH")) {
+ result = new BottomSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_SOUTH")) {
+ result = new TopSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_WEST")) {
+ result = new RightSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("SQUARE_CLOSEUP_EAST")) {
+ result = new LeftSquareCompartment(result, model);
+ } else if (type.equalsIgnoreCase("OVAL")) {
+ result = new OvalCompartment(result);
+ } else {
+ throw new InvalidXmlSchemaException("Unknown compartment type: " + type);
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("x", node));
+ result.setY(getNodeAttr("y", node));
+ result.setWidth(getNodeAttr("w", node));
+ result.setHeight(getNodeAttr("h", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:doubleLine")) {
+ result.setLineThickness(getNodeAttr("thickness", node));
+ result.setLineOuterWidth(getNodeAttr("outerWidth", node));
+ result.setLineInnerWidth(getNodeAttr("innerWidth", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
+ result.setColor(getCommonParser().getColor(node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+ // not handled
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:point")) {
+ if (result instanceof BottomSquareCompartment) {
+ result.setY(getNodeAttr("y", node));
+ } else if (result instanceof LeftSquareCompartment) {
+ result.setX(getNodeAttr("x", node));
+ } else if (result instanceof RightSquareCompartment) {
+ result.setX(getNodeAttr("x", node));
+ result.setWidth(result.getWidth() - result.getX());
+ } else if (result instanceof TopSquareCompartment) {
+ result.setY(getNodeAttr("y", node));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Don't know what to do with celldesigner:point for class: " + result.getClass());
+ }
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:namePoint")) {
+ result.setNamePoint(getCommonParser().getPosition(node));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:compartmentAlias: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public String toXml(Compartment compartment) {
+ StringBuilder sb = new StringBuilder("");
+
+ sb.append("<celldesigner:compartmentAlias ");
+ sb.append("id=\"" + compartment.getElementId() + "\" ");
+ sb.append("compartment=\"" + elements.getElementId(compartment) + "\">\n");
+
+ boolean bounds = true;
+
+ if (compartment.getClass().getName().equals(SquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE</celldesigner:class>\n");
+ } else if (compartment.getClass().getName().equals(OvalCompartment.class.getName())) {
+ sb.append("<celldesigner:class>OVAL</celldesigner:class>\n");
+ } else if (compartment.getClass().getName().equals(BottomSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_NORTH</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
+ } else if (compartment.getClass().getName().equals(TopSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_SOUTH</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"10\" y=\"" + compartment.getY() + "\"/>");
+ } else if (compartment.getClass().getName().equals(LeftSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_EAST</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"" + compartment.getWidth() + "\" y=\"10\"/>");
+ } else if (compartment.getClass().getName().equals(RightSquareCompartment.class.getName())) {
+ sb.append("<celldesigner:class>SQUARE_CLOSEUP_WEST</celldesigner:class>\n");
+ bounds = false;
+ sb.append("<celldesigner:point x=\"" + compartment.getX() + "\" y=\"10\"/>");
+ } else {
+ throw new NotImplementedException("Unknown compartment class: " + compartment.getClass());
+ }
+ if (bounds) {
+ sb.append("<celldesigner:bounds ");
+ sb.append("x=\"" + compartment.getX() + "\" ");
+ sb.append("y=\"" + compartment.getY() + "\" ");
+ sb.append("w=\"" + compartment.getWidth() + "\" ");
+ sb.append("h=\"" + compartment.getHeight() + "\"/>\n");
+ }
+
+ sb.append("<celldesigner:namePoint ");
+ sb.append("x=\"" + compartment.getNamePoint().getX() + "\" ");
+ sb.append("y=\"" + compartment.getNamePoint().getY() + "\"/>\n");
+
+ sb.append("<celldesigner:doubleLine ");
+ sb.append("thickness=\"" + compartment.getThickness() + "\" ");
+ sb.append("outerWidth=\"" + compartment.getOuterWidth() + "\" ");
+ sb.append("innerWidth=\"" + compartment.getInnerWidth() + "\"/>\n");
+
+ sb.append("<celldesigner:paint ");
+ sb.append("color=\"" + colorToString(compartment.getColor()) + "\" scheme=\"Color\"/>\n");
+
+ sb.append("</celldesigner:compartmentAlias>\n");
+
+ return sb.toString();
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
index e3b9b91842..3e3b7bc662 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParser.java
@@ -88,6 +88,7 @@ public class ComplexAliasXmlParser extends AbstractAliasXmlParser<Complex> {
throw new InvalidXmlSchemaException("No species with id=\"" + speciesId + "\" for complex alias \"" + aliasId + "\"");
}
Complex result = species.createModelElement(aliasId);
+ elements.addElement(species, aliasId);
String state = "usual";
NodeList nodes = aliasNode.getChildNodes();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
index b936673c9f..c92137511e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParser.java
@@ -26,223 +26,227 @@ import lcsb.mapviewer.model.map.species.Species;
* @see Complex
*/
public class SpeciesAliasXmlParser extends AbstractAliasXmlParser<Species> {
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
-
- /**
- * Collection of {@link CellDesignerElement cell designer elements} parsed
- * from xml.
- */
- private CellDesignerElementCollection elements;
-
- /**
- * Model for which we parse elements.
- */
- private Model model;
-
- /**
- * Default constructor with model object for which we parse data.
- *
- * @param model
- * model for which we parse elements
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
- */
- public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
- this.elements = elements;
- this.model = model;
- }
-
- @Override
- Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
-
- String speciesId = getNodeAttr("species", aliasNode);
- String aliasId = getNodeAttr("id", aliasNode);
- CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
- if (species == null) {
- throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
- }
- if (species instanceof CellDesignerComplexSpecies) {
- logger.warn("[" + speciesId + "," + aliasId + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
- }
-
- Species result = species.createModelElement(aliasId);
-
- String state = "usual";
- NodeList nodes = aliasNode.getChildNodes();
- View usualView = null;
- View briefView = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
- result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
- result.setX(getNodeAttr("X", node));
- result.setY(getNodeAttr("Y", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
- result.setFontSize(getNodeAttr("size", node));
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
- state = getNodeAttr("state", node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
- usualView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
- briefView = getCommonParser().getView(node);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
- processAliasState(node, result);
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- // not handled
- continue;
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
- }
- }
- }
-
- View view = null;
- if (state.equalsIgnoreCase("usual")) {
- view = usualView;
- } else if (state.equalsIgnoreCase("brief")) {
- view = briefView;
- }
-
- if (view != null) {
- // inner position defines the position in compartment
- // result.moveBy(view.innerPosition);
- result.setWidth(view.getBoxSize().width);
- result.setHeight(view.getBoxSize().height);
- result.setLineWidth(view.getSingleLine().getWidth());
- result.setColor(view.getColor());
- } else {
- throw new InvalidXmlSchemaException("No view in Alias");
- }
- result.setState(state);
- String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
- if (!compartmentAliasId.isEmpty()) {
- Compartment compartment = model.getElementByElementId(compartmentAliasId);
- if (compartment == null) {
- throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
- } else {
- result.setCompartment(compartment);
- compartment.addElement(result);
- }
- }
- String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
- if (!complexAliasId.isEmpty()) {
- Complex complex = model.getElementByElementId(complexAliasId);
- if (complex == null) {
- throw new InvalidXmlSchemaException("ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
- } else {
- result.setComplex(complex);
- complex.addSpecies(result);
- }
- }
- return result;
- }
-
- /**
- * Process node with information about alias state and puts data into alias.
- *
- * @param node
- * node where information about alias state is stored
- * @param alias
- * alias object to be modified if necessary
- */
- private void processAliasState(Node node, Species alias) {
- String state = getNodeAttr("state", node);
- if ("open".equalsIgnoreCase(state)) {
- String prefix = getNodeAttr("prefix", node);
- String label = getNodeAttr("label", node);
- alias.setStatePrefix(prefix);
- alias.setStateLabel(label);
- } else if ("empty".equalsIgnoreCase(state)) {
- return;
- } else if (state == null || state.isEmpty()) {
- return;
- } else {
- throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
- }
-
- }
-
- @Override
- public String toXml(Species species) {
- Compartment ca = null;
- // artifitial compartment aliases should be excluded
- if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
- ca = (Compartment) species.getCompartment();
- } else if (species.getComplex() == null) {
- ModelData model = species.getModelData();
- if (model != null) {
- for (Compartment cAlias : model.getModel().getCompartments()) {
- if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
- if (ca == null) {
- ca = cAlias;
- } else if (ca.getSize() > cAlias.getSize()) {
- ca = cAlias;
- }
- }
- }
- }
- }
-
- Complex complex = species.getComplex();
-
- String compartmentAliasId = null;
- if (ca != null) {
- compartmentAliasId = ca.getElementId();
- }
- StringBuilder sb = new StringBuilder("");
- sb.append("<celldesigner:speciesAlias ");
- sb.append("id=\"" + species.getElementId() + "\" ");
- sb.append("species=\"" + elements.getElementId(species) + "\" ");
- if (compartmentAliasId != null) {
- sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
- }
-
- if (complex != null) {
- sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
- }
- sb.append(">\n");
-
- if (species.getActivity() != null) {
- if (species.getActivity()) {
- sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
- } else {
- sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
- }
- }
-
- sb.append("<celldesigner:bounds ");
- sb.append("x=\"" + species.getX() + "\" ");
- sb.append("y=\"" + species.getY() + "\" ");
- sb.append("w=\"" + species.getWidth() + "\" ");
- sb.append("h=\"" + species.getHeight() + "\" ");
- sb.append("/>\n");
-
- sb.append("<celldesigner:font size=\"" + species.getFontSize() + "\"/>\n");
-
- // TODO to be improved
- sb.append("<celldesigner:view state=\"usual\"/>\n");
- sb.append("<celldesigner:usualView>");
- sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:usualView>\n");
- sb.append("<celldesigner:briefView>");
- sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
- sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
- sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
- sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
- sb.append("</celldesigner:briefView>\n");
- if (species.getStateLabel() != null || species.getStatePrefix() != null) {
- sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\"" + species.getStateLabel() + "\"/>\n");
- }
- sb.append("</celldesigner:speciesAlias>\n");
- return sb.toString();
- }
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class.getName());
+
+ /**
+ * Collection of {@link CellDesignerElement cell designer elements} parsed from
+ * xml.
+ */
+ private CellDesignerElementCollection elements;
+
+ /**
+ * Model for which we parse elements.
+ */
+ private Model model;
+
+ /**
+ * Default constructor with model object for which we parse data.
+ *
+ * @param model
+ * model for which we parse elements
+ * @param elements
+ * collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
+ */
+ public SpeciesAliasXmlParser(CellDesignerElementCollection elements, Model model) {
+ this.elements = elements;
+ this.model = model;
+ }
+
+ @Override
+ Species parseXmlAlias(Node aliasNode) throws InvalidXmlSchemaException {
+
+ String speciesId = getNodeAttr("species", aliasNode);
+ String aliasId = getNodeAttr("id", aliasNode);
+ CellDesignerSpecies<?> species = elements.getElementByElementId(speciesId);
+ if (species == null) {
+ throw new InvalidXmlSchemaException("Unknown species for alias (speciesId: " + speciesId + ")");
+ }
+ if (species instanceof CellDesignerComplexSpecies) {
+ logger.warn("[" + speciesId + "," + aliasId
+ + "]\tSpecies is defined as a complex, but alias is not a complex. Changing alias to complex.");
+ }
+
+ elements.addElement(species, aliasId);
+ Species result = species.createModelElement(aliasId);
+
+ String state = "usual";
+ NodeList nodes = aliasNode.getChildNodes();
+ View usualView = null;
+ View briefView = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:activity")) {
+ result.setActivity(getNodeValue(node).equalsIgnoreCase("active"));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:bounds")) {
+ result.setX(getNodeAttr("X", node));
+ result.setY(getNodeAttr("Y", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:font")) {
+ result.setFontSize(getNodeAttr("size", node));
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:view")) {
+ state = getNodeAttr("state", node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:usualView")) {
+ usualView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:briefView")) {
+ briefView = getCommonParser().getView(node);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:info")) {
+ processAliasState(node, result);
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
+ // not handled
+ continue;
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:speciesAlias: " + node.getNodeName());
+ }
+ }
+ }
+
+ View view = null;
+ if (state.equalsIgnoreCase("usual")) {
+ view = usualView;
+ } else if (state.equalsIgnoreCase("brief")) {
+ view = briefView;
+ }
+
+ if (view != null) {
+ // inner position defines the position in compartment
+ // result.moveBy(view.innerPosition);
+ result.setWidth(view.getBoxSize().width);
+ result.setHeight(view.getBoxSize().height);
+ result.setLineWidth(view.getSingleLine().getWidth());
+ result.setColor(view.getColor());
+ } else {
+ throw new InvalidXmlSchemaException("No view in Alias");
+ }
+ result.setState(state);
+ String compartmentAliasId = getNodeAttr("compartmentAlias", aliasNode);
+ if (!compartmentAliasId.isEmpty()) {
+ Compartment compartment = model.getElementByElementId(compartmentAliasId);
+ if (compartment == null) {
+ throw new InvalidXmlSchemaException("CompartmentAlias does not exist: " + compartmentAliasId);
+ } else {
+ result.setCompartment(compartment);
+ compartment.addElement(result);
+ }
+ }
+ String complexAliasId = getNodeAttr("complexSpeciesAlias", aliasNode);
+ if (!complexAliasId.isEmpty()) {
+ Complex complex = model.getElementByElementId(complexAliasId);
+ if (complex == null) {
+ throw new InvalidXmlSchemaException(
+ "ComplexAlias does not exist: " + complexAliasId + ", current: " + result.getElementId());
+ } else {
+ result.setComplex(complex);
+ complex.addSpecies(result);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Process node with information about alias state and puts data into alias.
+ *
+ * @param node
+ * node where information about alias state is stored
+ * @param alias
+ * alias object to be modified if necessary
+ */
+ private void processAliasState(Node node, Species alias) {
+ String state = getNodeAttr("state", node);
+ if ("open".equalsIgnoreCase(state)) {
+ String prefix = getNodeAttr("prefix", node);
+ String label = getNodeAttr("label", node);
+ alias.setStatePrefix(prefix);
+ alias.setStateLabel(label);
+ } else if ("empty".equalsIgnoreCase(state)) {
+ return;
+ } else if (state == null || state.isEmpty()) {
+ return;
+ } else {
+ throw new NotImplementedException("[Alias: " + alias.getElementId() + "] Unkown alias state: " + state);
+ }
+
+ }
+
+ @Override
+ public String toXml(Species species) {
+ Compartment ca = null;
+ // artificial compartment aliases should be excluded
+ if (species.getCompartment() != null && !(species.getCompartment() instanceof PathwayCompartment)) {
+ ca = (Compartment) species.getCompartment();
+ } else if (species.getComplex() == null) {
+ ModelData model = species.getModelData();
+ if (model != null) {
+ for (Compartment cAlias : model.getModel().getCompartments()) {
+ if (!(cAlias instanceof PathwayCompartment) && cAlias.cross(species)) {
+ if (ca == null) {
+ ca = cAlias;
+ } else if (ca.getSize() > cAlias.getSize()) {
+ ca = cAlias;
+ }
+ }
+ }
+ }
+ }
+
+ Complex complex = species.getComplex();
+
+ String compartmentAliasId = null;
+ if (ca != null) {
+ compartmentAliasId = ca.getElementId();
+ }
+ StringBuilder sb = new StringBuilder("");
+ sb.append("<celldesigner:speciesAlias ");
+ sb.append("id=\"" + species.getElementId() + "\" ");
+ sb.append("species=\"" + elements.getElementId(species) + "\" ");
+ if (compartmentAliasId != null) {
+ sb.append("compartmentAlias=\"" + compartmentAliasId + "\" ");
+ }
+
+ if (complex != null) {
+ sb.append("complexSpeciesAlias=\"" + complex.getElementId() + "\" ");
+ }
+ sb.append(">\n");
+
+ if (species.getActivity() != null) {
+ if (species.getActivity()) {
+ sb.append("<celldesigner:activity>active</celldesigner:activity>\n");
+ } else {
+ sb.append("<celldesigner:activity>inactive</celldesigner:activity>\n");
+ }
+ }
+
+ sb.append("<celldesigner:bounds ");
+ sb.append("x=\"" + species.getX() + "\" ");
+ sb.append("y=\"" + species.getY() + "\" ");
+ sb.append("w=\"" + species.getWidth() + "\" ");
+ sb.append("h=\"" + species.getHeight() + "\" ");
+ sb.append("/>\n");
+
+ sb.append("<celldesigner:font size=\"" + species.getFontSize() + "\"/>\n");
+
+ // TODO to be improved
+ sb.append("<celldesigner:view state=\"usual\"/>\n");
+ sb.append("<celldesigner:usualView>");
+ sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:usualView>\n");
+ sb.append("<celldesigner:briefView>");
+ sb.append("<celldesigner:innerPosition x=\"" + species.getX() + "\" y=\"" + species.getY() + "\"/>");
+ sb.append("<celldesigner:boxSize width=\"" + species.getWidth() + "\" height=\"" + species.getHeight() + "\"/>");
+ sb.append("<celldesigner:singleLine width=\"" + species.getLineWidth() + "\"/>");
+ sb.append("<celldesigner:paint color=\"" + colorToString(species.getColor()) + "\" scheme=\"Color\"/>");
+ sb.append("</celldesigner:briefView>\n");
+ if (species.getStateLabel() != null || species.getStatePrefix() != null) {
+ sb.append("<celldesigner:info state=\"open\" prefix=\"" + species.getStatePrefix() + "\" label=\""
+ + species.getStateLabel() + "\"/>\n");
+ }
+ sb.append("</celldesigner:speciesAlias>\n");
+ return sb.toString();
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 735682c067..c0a3ef113e 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -17,6 +17,7 @@ import org.w3c.dom.NodeList;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
@@ -35,6 +36,7 @@ import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.AndOperator;
@@ -136,13 +138,16 @@ public class ReactionFromXml extends XmlParser {
*/
private boolean sbgn;
+ CellDesignerElementCollection elements;
+
/**
* Default constructor.
*
* @param sbgn
* Should the converter use SBGN standard
*/
- public ReactionFromXml(boolean sbgn) {
+ public ReactionFromXml(CellDesignerElementCollection elements, boolean sbgn) {
+ this.elements = elements;
this.sbgn = sbgn;
}
@@ -153,7 +158,7 @@ public class ReactionFromXml extends XmlParser {
* xml node
* @param model
* model where the reaction is placed
- * @return reactin from xml node
+ * @return reaction from xml node
* @throws ReactionParserException
* thrown when the xml is invalid
* @throws InvalidXmlSchemaException
@@ -211,16 +216,25 @@ public class ReactionFromXml extends XmlParser {
private Map<String, Element> getSpeciesIdToElementMappingFromAnnotationNode(Node annotationNode, Model model) {
Map<String, Element> result = new HashMap<>();
-
+
List<Node> elementNodes = new ArrayList<>();
elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:baseReactant", annotationNode));
elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:baseProduct", annotationNode));
elementNodes.addAll(super.getAllNotNecessirellyDirectChild("celldesigner:linkTarget", annotationNode));
-
- for (Node node: elementNodes) {
+
+ for (Node node : elementNodes) {
String speciesId = super.getNodeAttr("species", node);
String aliasId = super.getNodeAttr("alias", node);
- result.put(speciesId, model.getElementByElementId(aliasId));
+ Element element = model.getElementByElementId(aliasId);
+ result.put(speciesId, element);
+
+ Compartment compartment = element.getCompartment();
+ if (compartment != null) {
+ // in kinetics we can have reference to compartment (so we need to find SBML
+ // compartment id)
+ String compartmentId = elements.getElementByElementId(compartment.getElementId()).getElementId();
+ result.put(compartmentId, compartment);
+ }
}
return result;
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
index 1bdd6a7a7a..96d37edc31 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java
@@ -35,14 +35,14 @@ public class ReactionXmlParser extends XmlParser {
* other parts of the model.
*
* @param sbgn
- * Should sbgn standard be used
+ * Should SBGN standard be used
* @param elements
* collection of {@link CellDesignerElement cell designer elements}
* parsed from xml
*/
public ReactionXmlParser(CellDesignerElementCollection elements, boolean sbgn) {
reactionToXml = new ReactionToXml(elements, sbgn);
- reactionFromXml = new ReactionFromXml(sbgn);
+ reactionFromXml = new ReactionFromXml(elements, sbgn);
}
/**
@@ -52,7 +52,7 @@ public class ReactionXmlParser extends XmlParser {
* xml node
* @param model
* model where the reaction is placed
- * @return reactin from xml node
+ * @return reaction from xml node
* @throws ReactionParserException
* thrown when the xml is invalid
* @throws InvalidXmlSchemaException
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
index c686ccb3cf..577844e965 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/structure/CellDesignerElement.java
@@ -14,13 +14,13 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.species.Element;
/**
- * Generic CellDesigner elementmap. It is a root object in inheritence three for
+ * Generic CellDesigner element map. It is a root object in inheritance three for
* every element ({@link CellDesignerSpecies} or {@link CellDesignerCompartment}
* ).
*
* @param <T>
- * type of the {@link Element} in the model that is desrbide byy this
- * celldesigner class
+ * type of the {@link Element} in the model that is describe by this
+ * CellDesigner class
* @author Piotr Gawron
*
*/
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
index bb1aa8ad25..e5b4e0509e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParserTest.java
@@ -5,6 +5,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
import java.util.List;
import org.apache.log4j.Logger;
@@ -20,320 +22,343 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompart
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGenericProtein;
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.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class AliasCollectionXmlParserTest extends CellDesignerTestFunctions {
- AliasCollectionXmlParser parser;
- Model model;
- CellDesignerElementCollection elements;
- Logger logger = Logger.getLogger(AliasCollectionXmlParserTest.class.getName());
-
- @Before
- public void setUp() throws Exception {
- model = new ModelFullIndexed(null);
-
- elements = new CellDesignerElementCollection();
-
- parser = new AliasCollectionXmlParser(elements, model);
-
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlSpeciesAliasCollection() throws Exception {
- try {
- elements.addElement(new CellDesignerGenericProtein("s2594"));
- elements.addElement(new CellDesignerGenericProtein("s2595"));
- elements.addElement(new CellDesignerGenericProtein("s2596"));
- elements.addElement(new CellDesignerGenericProtein("s2506"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(4, list.size());
- Species aliasSa8 = null;
- Species aliasSa9 = null;
- Species aliasSa10 = null;
- Species aliasSa11 = null;
- for (Species alias : list) {
- if (alias.getElementId().equals("sa8"))
- aliasSa8 = alias;
- if (alias.getElementId().equals("sa9"))
- aliasSa9 = alias;
- if (alias.getElementId().equals("sa10"))
- aliasSa10 = alias;
- if (alias.getElementId().equals("sa11"))
- aliasSa11 = alias;
- }
- assertNotNull(aliasSa8);
- assertNotNull(aliasSa9);
- assertNotNull(aliasSa10);
- assertNotNull(aliasSa11);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlSpeciesAliasCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlSpeciesAliasCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfSpeciesAliases"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlComplexAliasCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/complex_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlComplexAliasCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:listOfComplexSpeciesAliases"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlCompartmentAliasCollection() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/compartment_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- parser.parseXmlCompartmentAliasCollection(node);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:listOfCompartmentAliases"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesAliasCollectionToXmlString() throws Exception {
- try {
- elements.addElement(new CellDesignerGenericProtein("s2594"));
- elements.addElement(new CellDesignerGenericProtein("s2506"));
- elements.addElement(new CellDesignerGenericProtein("s2595"));
- elements.addElement(new CellDesignerGenericProtein("s2596"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
- assertEquals(0, getWarnings().size());
- String xmlString2 = parser.speciesAliasCollectionToXmlString(list);
- assertNotNull(xmlString2);
-
- // add position to elements list, because parser forgot CD ids and created
- // new for them
- for (Species alias : list) {
- elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
- }
-
- node = getNodeFromXmlString(xmlString2);
- list = parser.parseXmlSpeciesAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(4, list.size());
- Species aliasSa8 = null;
- Species aliasSa9 = null;
- Species aliasSa10 = null;
- Species aliasSa11 = null;
- for (Species alias : list) {
- if (alias.getElementId().equals("sa8"))
- aliasSa8 = alias;
- if (alias.getElementId().equals("sa9"))
- aliasSa9 = alias;
- if (alias.getElementId().equals("sa10"))
- aliasSa10 = alias;
- if (alias.getElementId().equals("sa11"))
- aliasSa11 = alias;
- }
- assertNotNull(aliasSa8);
- assertNotNull(aliasSa9);
- assertNotNull(aliasSa10);
- assertNotNull(aliasSa11);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlComplexAliasCollection() throws Exception {
- try {
- elements.addElement(new CellDesignerComplexSpecies("s2597"));
- elements.addElement(new CellDesignerComplexSpecies("s2598"));
- elements.addElement(new CellDesignerComplexSpecies("s2599"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Complex> list = parser.parseXmlComplexAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- Complex aliasSa1 = null;
- Complex aliasSa2 = null;
- Complex aliasSa3 = null;
- for (Complex alias : list) {
- if (alias.getElementId().equals("csa1"))
- aliasSa1 = alias;
- if (alias.getElementId().equals("csa2"))
- aliasSa2 = alias;
- if (alias.getElementId().equals("csa3"))
- aliasSa3 = alias;
- }
- assertNotNull(aliasSa1);
- assertNotNull(aliasSa2);
- assertNotNull(aliasSa3);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testComplexAliasCollectionToXmlString() throws Exception {
- try {
- elements.addElement(new CellDesignerComplexSpecies("s2597"));
- elements.addElement(new CellDesignerComplexSpecies("s2598"));
- elements.addElement(new CellDesignerComplexSpecies("s2599"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Complex> list = parser.parseXmlComplexAliasCollection(node);
- assertEquals(0, getWarnings().size());
- String xmlString2 = parser.complexAliasCollectionToXmlString(list);
- assertNotNull(xmlString2);
-
- // add position to elements list, because parser forgot CD ids and created
- // new for them
- for (Complex complexAlias : list) {
- elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complexAlias)));
- }
-
- node = getNodeFromXmlString(xmlString2);
- list = parser.parseXmlComplexAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- Complex aliasSa1 = null;
- Complex aliasSa2 = null;
- Complex aliasSa3 = null;
- for (Complex alias : list) {
- if (alias.getElementId().equals("csa1"))
- aliasSa1 = alias;
- if (alias.getElementId().equals("csa2"))
- aliasSa2 = alias;
- if (alias.getElementId().equals("csa3"))
- aliasSa3 = alias;
- }
- assertNotNull(aliasSa1);
- assertNotNull(aliasSa2);
- assertNotNull(aliasSa3);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlCompartmentAliasCollection() throws Exception {
- try {
- elements.addElement(new CellDesignerCompartment("c1"));
- elements.addElement(new CellDesignerCompartment("c2"));
- elements.addElement(new CellDesignerCompartment("c3"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
- assertEquals(0, getWarnings().size());
- assertNotNull(list);
- assertEquals(3, list.size());
- Compartment aliasCa1 = null;
- Compartment aliasCa2 = null;
- Compartment aliasCa3 = null;
- for (Compartment alias : list) {
- if (alias.getElementId().equals("ca1"))
- aliasCa1 = alias;
- if (alias.getElementId().equals("ca2"))
- aliasCa2 = alias;
- if (alias.getElementId().equals("ca3"))
- aliasCa3 = alias;
- }
- assertNotNull(aliasCa1);
- assertNotNull(aliasCa2);
- assertNotNull(aliasCa3);
-
- } catch (Exception e) {
- throw e;
- }
- }
-
- @Test
- public void testCompartmentAliasCollectionToXmlString() throws Exception {
- try {
- elements.addElement(new CellDesignerCompartment("c1"));
- elements.addElement(new CellDesignerCompartment("c2"));
- elements.addElement(new CellDesignerCompartment("c3"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
- Node node = getNodeFromXmlString(xmlString);
- List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
- assertEquals(0, getWarnings().size());
-
- String xmlString2 = parser.compartmentAliasCollectionToXmlString(list);
- assertNotNull(xmlString2);
-
- // add position to elements list, because parser forgot CD ids and created
- // new for them
- for (Compartment alias : list) {
- elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
- }
-
- node = getNodeFromXmlString(xmlString2);
- list = parser.parseXmlCompartmentAliasCollection(node);
- assertEquals(0, getWarnings().size());
-
- assertNotNull(list);
- assertEquals(3, list.size());
- Compartment aliasSa1 = null;
- Compartment aliasSa2 = null;
- Compartment aliasSa3 = null;
- for (Compartment alias : list) {
- if (alias.getElementId().equals("ca1"))
- aliasSa1 = alias;
- if (alias.getElementId().equals("ca2"))
- aliasSa2 = alias;
- if (alias.getElementId().equals("ca3"))
- aliasSa3 = alias;
- }
- assertNotNull(aliasSa1);
- assertNotNull(aliasSa2);
- assertNotNull(aliasSa3);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ AliasCollectionXmlParser parser;
+ Model model;
+ CellDesignerElementCollection elements;
+ Logger logger = Logger.getLogger(AliasCollectionXmlParserTest.class.getName());
+
+ @Before
+ public void setUp() throws Exception {
+ model = new ModelFullIndexed(null);
+
+ elements = new CellDesignerElementCollection();
+
+ parser = new AliasCollectionXmlParser(elements, model);
+
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlSpeciesAliasCollection() throws Exception {
+ try {
+ elements.addElement(new CellDesignerGenericProtein("s2594"));
+ elements.addElement(new CellDesignerGenericProtein("s2595"));
+ elements.addElement(new CellDesignerGenericProtein("s2596"));
+ elements.addElement(new CellDesignerGenericProtein("s2506"));
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(4, list.size());
+ Species aliasSa8 = null;
+ Species aliasSa9 = null;
+ Species aliasSa10 = null;
+ Species aliasSa11 = null;
+ for (Species alias : list) {
+ if (alias.getElementId().equals("sa8"))
+ aliasSa8 = alias;
+ if (alias.getElementId().equals("sa9"))
+ aliasSa9 = alias;
+ if (alias.getElementId().equals("sa10"))
+ aliasSa10 = alias;
+ if (alias.getElementId().equals("sa11"))
+ aliasSa11 = alias;
+ }
+ assertNotNull(aliasSa8);
+ assertNotNull(aliasSa9);
+ assertNotNull(aliasSa10);
+ assertNotNull(aliasSa11);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlSpeciesAliasCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlSpeciesAliasCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:listOfSpeciesAliases"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlComplexAliasCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/complex_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlComplexAliasCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfComplexSpeciesAliases"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlCompartmentAliasCollection() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/compartment_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ parser.parseXmlCompartmentAliasCollection(node);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfCompartmentAliases"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesAliasCollectionToXmlString() throws Exception {
+ try {
+ List<Species> originalLlist = createSpeciesList();
+ String xmlString2 = parser.speciesAliasCollectionToXmlString(originalLlist);
+ assertNotNull(xmlString2);
+
+ for (Species alias : originalLlist) {
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
+ }
+
+ Node node = getNodeFromXmlString(xmlString2);
+ List<Species> list = parser.parseXmlSpeciesAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ for (Species species : originalLlist) {
+ boolean found = false;
+ for (Species alias : list) {
+ if (alias.getElementId().equals(species.getElementId())) {
+ found = true;
+ }
+ }
+ assertTrue(found);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<Species> createSpeciesList() {
+ List<Species> result = new ArrayList<>();
+ result.add(createProtein("sa1"));
+ result.add(createProtein("sa2"));
+ result.add(createProtein("sa3"));
+ return result;
+ }
+
+ private Species createProtein(String id) {
+ GenericProtein protein = new GenericProtein(id);
+ protein.setActivity(true);
+ protein.setFontSize(4);
+ protein.setHeight(10);
+ protein.setWidth(20);
+ protein.setX(30);
+ protein.setY(40);
+ protein.setName(id + "name");
+ protein.setStateLabel("xxx");
+ protein.setStatePrefix("yyy");
+ return protein;
+ }
+
+ @Test
+ public void testParseXmlComplexAliasCollection() throws Exception {
+ try {
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
+ elements.addElement(new CellDesignerComplexSpecies("s2598"));
+ elements.addElement(new CellDesignerComplexSpecies("s2599"));
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Complex> list = parser.parseXmlComplexAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ Complex aliasSa1 = null;
+ Complex aliasSa2 = null;
+ Complex aliasSa3 = null;
+ for (Complex alias : list) {
+ if (alias.getElementId().equals("csa1"))
+ aliasSa1 = alias;
+ if (alias.getElementId().equals("csa2"))
+ aliasSa2 = alias;
+ if (alias.getElementId().equals("csa3"))
+ aliasSa3 = alias;
+ }
+ assertNotNull(aliasSa1);
+ assertNotNull(aliasSa2);
+ assertNotNull(aliasSa3);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexAliasCollectionToXmlString() throws Exception {
+ try {
+ List<Complex> list = createComplexAliasList();
+ String xmlString2 = parser.complexAliasCollectionToXmlString(list);
+ assertNotNull(xmlString2);
+
+ for (Complex complexAlias : list) {
+ elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complexAlias)));
+ }
+
+ Node node = getNodeFromXmlString(xmlString2);
+ list = parser.parseXmlComplexAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ Complex aliasSa1 = null;
+ Complex aliasSa2 = null;
+ Complex aliasSa3 = null;
+ for (Complex alias : list) {
+ if (alias.getElementId().equals("csa1"))
+ aliasSa1 = alias;
+ if (alias.getElementId().equals("csa2"))
+ aliasSa2 = alias;
+ if (alias.getElementId().equals("csa3"))
+ aliasSa3 = alias;
+ }
+ assertNotNull(aliasSa1);
+ assertNotNull(aliasSa2);
+ assertNotNull(aliasSa3);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<Complex> createComplexAliasList() {
+ List<Complex> result = new ArrayList<>();
+ result.add(createComplex("csa1"));
+ result.add(createComplex("csa2"));
+ result.add(createComplex("csa3"));
+ return result;
+ }
+
+ private Complex createComplex(String id) {
+ Complex complex = new Complex(id);
+ complex.setFontSize(13.5);
+ complex.setHeight(90);
+ complex.setWidth(80);
+ complex.setName("name_112_" + id);
+ complex.setX(32);
+ complex.setY(42);
+ return complex;
+ }
+
+ @Test
+ public void testParseXmlCompartmentAliasCollection() throws Exception {
+ try {
+ elements.addElement(new CellDesignerCompartment("c1"));
+ elements.addElement(new CellDesignerCompartment("c2"));
+ elements.addElement(new CellDesignerCompartment("c3"));
+
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(list);
+ assertEquals(3, list.size());
+ Compartment aliasCa1 = null;
+ Compartment aliasCa2 = null;
+ Compartment aliasCa3 = null;
+ for (Compartment alias : list) {
+ if (alias.getElementId().equals("ca1"))
+ aliasCa1 = alias;
+ if (alias.getElementId().equals("ca2"))
+ aliasCa2 = alias;
+ if (alias.getElementId().equals("ca3"))
+ aliasCa3 = alias;
+ }
+ assertNotNull(aliasCa1);
+ assertNotNull(aliasCa2);
+ assertNotNull(aliasCa3);
+
+ } catch (Exception e) {
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCompartmentAliasCollectionToXmlString() throws Exception {
+ try {
+ List<Compartment> originalLlist = createCompartmentList();
+ for (Compartment alias : originalLlist) {
+ elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
+ }
+
+ String xmlString2 = parser.compartmentAliasCollectionToXmlString(originalLlist);
+
+ Node node = getNodeFromXmlString(xmlString2);
+ List<Compartment> list = parser.parseXmlCompartmentAliasCollection(node);
+ assertEquals(0, getWarnings().size());
+
+ assertNotNull(list);
+ assertEquals(originalLlist.size(), list.size());
+ for (Compartment species : originalLlist) {
+ boolean found = false;
+ for (Compartment alias : list) {
+ if (alias.getElementId().equals(species.getElementId())) {
+ found = true;
+ }
+ }
+ assertTrue(found);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private List<Compartment> createCompartmentList() {
+ List<Compartment> result = new ArrayList<>();
+ result.add(createCompartment("ca1"));
+ result.add(createCompartment("ca2"));
+ result.add(createCompartment("ca3"));
+ return result;
+ }
+
+ private Compartment createCompartment(String id) {
+ Compartment compartment = new SquareCompartment(id);
+ compartment.setName("name" + id);
+ compartment.setX(13);
+ compartment.setY(14);
+ compartment.setWidth(100);
+ compartment.setHeight(120);
+ compartment.setNamePoint(new Point2D.Double(0, 1));
+
+ return compartment;
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
index 45cfe9ee61..c0b01bb7d8 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/CompartmentAliasXmlParserTest.java
@@ -6,6 +6,8 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import java.awt.geom.Point2D;
+
import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
@@ -27,231 +29,238 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
public class CompartmentAliasXmlParserTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class);
-
- CompartmentAliasXmlParser parser;
- Model model;
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- model = new ModelFullIndexed(null);
- elements = new CellDesignerElementCollection();
- parser = new CompartmentAliasXmlParser(elements, model);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- elements.addElement(new CellDesignerCompartment("c1"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- Compartment alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertEquals(0, getWarnings().size());
- String xmlString2 = parser.toXml(alias);
- assertNotNull(xmlString2);
-
- elements.addElement(new CellDesignerCompartment(elements.getElementId(alias)));
-
- Compartment alias2 = parser.parseXmlAlias(xmlString2);
- assertEquals(0, getWarnings().size());
-
- assertEquals(alias.getElementId(), alias2.getElementId());
- assertNotNull(alias.getName());
- assertEquals(alias.getFontSize(), alias2.getFontSize(), 1e-6);
- assertEquals(alias.getHeight(), alias2.getHeight(), 1e-6);
- assertEquals(alias.getWidth(), alias2.getWidth(), 1e-6);
- assertEquals(alias.getX(), alias2.getX(), 1e-6);
- assertEquals(alias.getY(), alias2.getY(), 1e-6);
- assertEquals(alias.getNamePoint().getX(), alias2.getNamePoint().getX(), 1e-6);
- assertEquals(alias.getNamePoint().getY(), alias2.getNamePoint().getY(), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Compartment does not exist in a model"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias2() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerCompartment comp = new CellDesignerCompartment();
- comp.setElementId("c1");
- elements.addElement(comp);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/invalid/compartment_alias.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown compartment type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias3() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerCompartment comp = new CellDesignerCompartment();
- comp.setElementId("c1");
- elements.addElement(comp);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/invalid/compartment_alias2.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Don't know what to do with celldesigner:point for class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void parseInvalidAlias4() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
- CellDesignerCompartment comp = new CellDesignerCompartment();
- comp.setElementId("c1");
- elements.addElement(comp);
- parser = new CompartmentAliasXmlParser(elements, model);
- String xmlString = readFile("testFiles/invalid/compartment_alias3.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expceted");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:compartmentAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasNode() throws Exception {
- try {
- elements.addElement(new CellDesignerCompartment("c1"));
-
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
- Compartment alias = (Compartment) parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertNotNull(alias);
- assertEquals("ca1", alias.getElementId());
- assertNotNull(alias.getName());
- assertTrue(alias instanceof SquareCompartment);
- assertEquals(139.0, alias.getX(), 1e-6);
- assertEquals(55.0, alias.getY(), 1e-6);
- assertEquals(522.0, alias.getWidth(), 1e-6);
- assertEquals(392.5, alias.getNamePoint().getX(), 1e-6);
- assertEquals(196.5, alias.getNamePoint().getY(), 1e-6);
- assertEquals(0xffcccc00, alias.getColor().getRGB());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() {
- try {
- parser.setCommonParser(null);
-
- assertNull(parser.getCommonParser());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLeftToXml() throws Exception {
- try {
- Compartment alias = new LeftSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testRightToXml() throws Exception {
- try {
- Compartment alias = new RightSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testTopToXml() throws Exception {
- try {
- Compartment alias = new TopSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testBotttomToXml() throws Exception {
- try {
- Compartment alias = new BottomSquareCompartment("id");
- String xml = parser.toXml(alias);
- assertNotNull(xml);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
- @Test
- public void testUnknownToXml() throws Exception {
- try {
- Compartment alias = Mockito.mock(BottomSquareCompartment.class);
- Mockito.when(alias.getElementId()).thenReturn("some id");
- parser.toXml(alias);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unknown compartment class"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
+ static Logger logger = Logger.getLogger(CompartmentAliasXmlParser.class);
+
+ CompartmentAliasXmlParser parser;
+ Model model;
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ model = new ModelFullIndexed(null);
+ elements = new CellDesignerElementCollection();
+ parser = new CompartmentAliasXmlParser(elements, model);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ Compartment compartment = createCompartment();
+ String xmlString = parser.toXml(compartment);
+ assertNotNull(xmlString);
+
+ elements.addElement(new CellDesignerCompartment(elements.getElementId(compartment)));
+
+ Compartment alias2 = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals(compartment.getElementId(), alias2.getElementId());
+ assertNotNull(compartment.getName());
+ assertEquals(compartment.getFontSize(), alias2.getFontSize(), 1e-6);
+ assertEquals(compartment.getHeight(), alias2.getHeight(), 1e-6);
+ assertEquals(compartment.getWidth(), alias2.getWidth(), 1e-6);
+ assertEquals(compartment.getX(), alias2.getX(), 1e-6);
+ assertEquals(compartment.getY(), alias2.getY(), 1e-6);
+ assertEquals(compartment.getNamePoint().getX(), alias2.getNamePoint().getX(), 1e-6);
+ assertEquals(compartment.getNamePoint().getY(), alias2.getNamePoint().getY(), 1e-6);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Compartment createCompartment() {
+ Compartment compartment = new SquareCompartment("comp_id");
+ compartment.setName("name");
+ compartment.setX(13);
+ compartment.setY(14);
+ compartment.setWidth(100);
+ compartment.setHeight(120);
+ compartment.setNamePoint(new Point2D.Double(0, 1));
+
+ return compartment;
+ }
+
+ @Test
+ public void parseInvalidAlias() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Compartment does not exist in a model"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void parseInvalidAlias2() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerCompartment comp = new CellDesignerCompartment();
+ comp.setElementId("c1");
+ elements.addElement(comp);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/invalid/compartment_alias.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown compartment type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void parseInvalidAlias3() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerCompartment comp = new CellDesignerCompartment();
+ comp.setElementId("c1");
+ elements.addElement(comp);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/invalid/compartment_alias2.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do with celldesigner:point for class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void parseInvalidAlias4() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ CellDesignerCompartment comp = new CellDesignerCompartment();
+ comp.setElementId("c1");
+ elements.addElement(comp);
+ parser = new CompartmentAliasXmlParser(elements, model);
+ String xmlString = readFile("testFiles/invalid/compartment_alias3.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expceted");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:compartmentAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasNode() throws Exception {
+ try {
+ elements.addElement(new CellDesignerCompartment("c1"));
+
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_compartment_alias.xml");
+ Compartment alias = (Compartment) parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(alias);
+ assertEquals("ca1", alias.getElementId());
+ assertNotNull(alias.getName());
+ assertTrue(alias instanceof SquareCompartment);
+ assertEquals(139.0, alias.getX(), 1e-6);
+ assertEquals(55.0, alias.getY(), 1e-6);
+ assertEquals(522.0, alias.getWidth(), 1e-6);
+ assertEquals(392.5, alias.getNamePoint().getX(), 1e-6);
+ assertEquals(196.5, alias.getNamePoint().getY(), 1e-6);
+ assertEquals(0xffcccc00, alias.getColor().getRGB());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() {
+ try {
+ parser.setCommonParser(null);
+
+ assertNull(parser.getCommonParser());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLeftToXml() throws Exception {
+ try {
+ Compartment alias = new LeftSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testRightToXml() throws Exception {
+ try {
+ Compartment alias = new RightSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testTopToXml() throws Exception {
+ try {
+ Compartment alias = new TopSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testBotttomToXml() throws Exception {
+ try {
+ Compartment alias = new BottomSquareCompartment("id");
+ String xml = parser.toXml(alias);
+ assertNotNull(xml);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testUnknownToXml() throws Exception {
+ try {
+ Compartment alias = Mockito.mock(BottomSquareCompartment.class);
+ Mockito.when(alias.getElementId()).thenReturn("some id");
+ parser.toXml(alias);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Unknown compartment class"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
index c129a0ac83..2864a26ee2 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/ComplexAliasXmlParserTest.java
@@ -7,6 +7,7 @@ import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
@@ -15,66 +16,74 @@ import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
public class ComplexAliasXmlParserTest extends CellDesignerTestFunctions {
- Model model;
- private ComplexAliasXmlParser parser;
- CellDesignerElementCollection elements;
+ Model model;
+ private ComplexAliasXmlParser parser;
+ CellDesignerElementCollection elements;
- @Before
- public void setUp() throws Exception {
- model = new ModelFullIndexed(null);
- elements = new CellDesignerElementCollection();
- parser = new ComplexAliasXmlParser(elements, model);
- }
+ @Before
+ public void setUp() throws Exception {
+ model = new ModelFullIndexed(null);
+ elements = new CellDesignerElementCollection();
+ parser = new ComplexAliasXmlParser(elements, model);
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testToXml() throws Exception {
- try {
- elements.addElement(new CellDesignerComplexSpecies("s2597"));
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
- Complex alias = (Complex) parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- String xmlString2 = parser.toXml(alias);
- assertNotNull(xmlString2);
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ Complex complex = createComplex();
+ String xmlString = parser.toXml(complex);
+ assertNotNull(xmlString);
- elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(alias)));
- Complex alias2 = (Complex) parser.parseXmlAlias(xmlString2);
- assertEquals(0, getWarnings().size());
+ elements.addElement(new CellDesignerComplexSpecies(elements.getElementId(complex)));
+ Complex complexFromXml = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
- assertEquals(alias.getElementId(), alias2.getElementId());
- assertNotNull(alias.getName());
- assertEquals(alias.getFontSize(), alias2.getFontSize(), 1e-6);
- assertEquals(alias.getHeight(), alias2.getHeight(), 1e-6);
- assertEquals(alias.getWidth(), alias2.getWidth(), 1e-6);
- assertEquals(alias.getX(), alias2.getX(), 1e-6);
- assertEquals(alias.getY(), alias2.getY(), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(complex.getElementId(), complexFromXml.getElementId());
+ assertNotNull(complex.getName());
+ assertEquals(complex.getFontSize(), complexFromXml.getFontSize(), Configuration.EPSILON);
+ assertEquals(complex.getHeight(), complexFromXml.getHeight(), Configuration.EPSILON);
+ assertEquals(complex.getWidth(), complexFromXml.getWidth(), Configuration.EPSILON);
+ assertEquals(complex.getX(), complexFromXml.getX(), Configuration.EPSILON);
+ assertEquals(complex.getY(), complexFromXml.getY(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testParseXmlAliasNode() throws Exception {
- try {
- elements.addElement(new CellDesignerComplexSpecies("s2597"));
+ private Complex createComplex() {
+ Complex complex = new Complex("id");
+ complex.setFontSize(13.5);
+ complex.setHeight(90);
+ complex.setWidth(80);
+ complex.setName("112");
+ complex.setX(32);
+ complex.setY(42);
+ return complex;
+ }
- String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
- Complex alias = (Complex) parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertEquals(false, alias.getActivity());
- assertEquals("csa1", alias.getElementId());
- assertEquals(12.0, alias.getFontSize(), 1e-6);
- assertEquals(120.0, alias.getHeight(), 1e-6);
- assertEquals(100.0, alias.getWidth(), 1e-6);
- assertEquals(744.0, alias.getX(), 1e-6);
- assertEquals(0.0, alias.getY(), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void testParseXmlAliasNode() throws Exception {
+ try {
+ elements.addElement(new CellDesignerComplexSpecies("s2597"));
+
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/cd_complex_alias.xml");
+ Complex alias = (Complex) parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertEquals(false, alias.getActivity());
+ assertEquals("csa1", alias.getElementId());
+ assertEquals(12.0, alias.getFontSize(), Configuration.EPSILON);
+ assertEquals(120.0, alias.getHeight(), Configuration.EPSILON);
+ assertEquals(100.0, alias.getWidth(), Configuration.EPSILON);
+ assertEquals(744.0, alias.getX(), Configuration.EPSILON);
+ assertEquals(0.0, alias.getY(), Configuration.EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
index eb9952801d..64bacf8376 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/alias/SpeciesAliasXmlParserTest.java
@@ -27,300 +27,310 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class SpeciesAliasXmlParserTest extends CellDesignerTestFunctions {
- static Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class);
-
- Model model;
- private SpeciesAliasXmlParser parser;
-
- private String testCompartmentAliasId2 = "s3";
- private String testCompartmentAliasId = "s4";
- private String testSpeciesId = "s5";
- private String testAliasId = "s6";
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
-
- model = createStubModel();
-
- CellDesignerGenericProtein species = new CellDesignerGenericProtein();
- species.setElementId("s78");
- elements.addElement(species);
-
- parser = new SpeciesAliasXmlParser(elements, model);
- }
-
- private Model createStubModel() {
- Model model = new ModelFullIndexed(null);
- model.addElement(new Compartment("ca1"));
- return model;
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testParseXmlAliasNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertEquals(false, alias.getActivity());
- assertEquals("sa36", alias.getElementId());
- assertEquals(16.0, alias.getFontSize(), 1e-6);
- assertEquals(25.0, alias.getHeight(), 1e-6);
- assertEquals(80, alias.getWidth(), 1e-6);
- assertEquals(11813.0, alias.getX(), 1e-6);
- assertEquals(2840.5, alias.getY(), 1e-6);
- assertEquals("ca1", alias.getCompartment().getElementId());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasFont() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_font.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(30.0, alias.getFontSize(), 1e-6);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXml() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- String xmlString2 = parser.toXml(alias);
- assertNotNull(xmlString2);
-
- elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
-
- Model model2 = createStubModel();
-
- parser = new SpeciesAliasXmlParser(elements, model2);
- Species alias2 = parser.parseXmlAlias(xmlString2);
- assertEquals(0, getWarnings().size());
-
- assertEquals(alias.getActivity(), alias2.getActivity());
- assertEquals(alias.getElementId(), alias2.getElementId());
- assertEquals(alias.getFontSize(), alias2.getFontSize(), 1e-6);
- assertEquals(alias.getHeight(), alias2.getHeight(), 1e-6);
- assertEquals(alias.getWidth(), alias2.getWidth(), 1e-6);
- assertEquals(alias.getX(), alias2.getX(), 1e-6);
- assertEquals(alias.getY(), alias2.getY(), 1e-6);
- assertEquals(alias.getCompartment().getElementId(), alias2.getCompartment().getElementId());
- assertEquals("Alias state label different", alias.getStateLabel(), alias2.getStateLabel());
- assertEquals("Alias state prefix different", alias.getStatePrefix(), alias2.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlAliasWithStateNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- String xmlString2 = parser.toXml(alias);
- assertNotNull(xmlString2);
-
- elements.addElement(new CellDesignerGenericProtein(elements.getElementId(alias)));
- Species alias2 = parser.parseXmlAlias(xmlString2);
- assertEquals(0, getWarnings().size());
-
- assertEquals("Alias state label different", alias.getStateLabel(), alias2.getStateLabel());
- assertEquals("Alias state prefix different", alias.getStatePrefix(), alias2.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasWithStateNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertNotNull(alias);
- assertEquals("test", alias.getStateLabel());
- assertEquals("free input", alias.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseXmlAliasWithoutStateNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_without_state.xml");
- Species alias = parser.parseXmlAlias(xmlString);
- assertEquals(0, getWarnings().size());
- assertNotNull(alias);
- assertNull(alias.getStateLabel());
- assertNull(alias.getStatePrefix());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown species for alias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode2() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias2.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:speciesAlias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode3() throws Exception {
- try {
- String xmlString = readFile("testFiles/invalid/species_alias3.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("No view in Alias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode4() throws Exception {
- try {
- parser = new SpeciesAliasXmlParser(elements, model);
-
- String xmlString = readFile("testFiles/invalid/species_alias4.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("CompartmentAlias does not exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode5() throws Exception {
- try {
- parser = new SpeciesAliasXmlParser(elements, model);
-
- String xmlString = readFile("testFiles/invalid/species_alias5.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (InvalidXmlSchemaException e) {
- assertTrue(e.getMessage().contains("ComplexAlias does not exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidXmlAliasNode6() throws Exception {
- try {
- parser = new SpeciesAliasXmlParser(elements, model);
-
- String xmlString = readFile("testFiles/invalid/species_alias6.xml");
- parser.parseXmlAlias(xmlString);
- fail("Exception expected");
- } catch (NotImplementedException e) {
- assertTrue(e.getMessage().contains("Unkown alias state"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testToXmlWithUnknownCompartment() throws Exception {
- try {
- Model model = Mockito.mock(ModelFullIndexed.class);
- ModelData md = new ModelData();
- md.setModel(model);
-
- Compartment ca2 = new Compartment(testCompartmentAliasId2);
- ca2.setElementId(testCompartmentAliasId2);
- ca2.setX(6);
- ca2.setY(6);
- ca2.setWidth(190);
- ca2.setHeight(190);
-
- Compartment ca = new Compartment(testCompartmentAliasId);
- ca.setElementId(testCompartmentAliasId);
- ca.setX(5);
- ca.setY(5);
- ca.setWidth(200);
- ca.setHeight(200);
-
- List<Compartment> list = new ArrayList<>();
- list.add(ca);
- list.add(ca2);
-
- // ensure that we return list (firts bigger compartment, then smaller)
- when(model.getCompartments()).thenReturn(list);
- when(model.getModelData()).thenReturn(md);
-
- Species alias = new Complex(testAliasId);
- alias.setX(10);
- alias.setY(10);
- alias.setWidth(100);
- alias.setHeight(100);
- alias.setModel(model);
- alias.setActivity(true);
-
- elements.addElement(new CellDesignerComplexSpecies(testSpeciesId));
- model.addElement(alias);
- SpeciesAliasXmlParser parser = new SpeciesAliasXmlParser(elements, model);
-
- String xml = parser.toXml(alias);
-
- assertTrue(xml.contains(testAliasId));
- assertTrue(xml.contains(testCompartmentAliasId2));
- assertTrue(xml.contains("<celldesigner:activity>active</celldesigner:activity>"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ static Logger logger = Logger.getLogger(SpeciesAliasXmlParser.class);
+
+ Model model;
+ private SpeciesAliasXmlParser parser;
+
+ private String testCompartmentAliasId2 = "s3";
+ private String testCompartmentAliasId = "s4";
+ private String testSpeciesId = "s5";
+ private String testAliasId = "s6";
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+
+ model = createStubModel();
+
+ CellDesignerGenericProtein species = new CellDesignerGenericProtein();
+ species.setElementId("s78");
+ elements.addElement(species);
+
+ parser = new SpeciesAliasXmlParser(elements, model);
+ }
+
+ private Model createStubModel() {
+ Model model = new ModelFullIndexed(null);
+ model.addElement(new Compartment("ca1"));
+ return model;
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testParseXmlAliasNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertEquals(false, alias.getActivity());
+ assertEquals("sa36", alias.getElementId());
+ assertEquals(16.0, alias.getFontSize(), 1e-6);
+ assertEquals(25.0, alias.getHeight(), 1e-6);
+ assertEquals(80, alias.getWidth(), 1e-6);
+ assertEquals(11813.0, alias.getX(), 1e-6);
+ assertEquals(2840.5, alias.getY(), 1e-6);
+ assertEquals("ca1", alias.getCompartment().getElementId());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasFont() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_font.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(30.0, alias.getFontSize(), 1e-6);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXml() throws Exception {
+ try {
+ Model model2 = createStubModel();
+ Species protein = createProtein();
+ protein.setCompartment(model2.getCompartments().iterator().next());
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(protein)));
+ String xmlString = parser.toXml(protein);
+
+ parser = new SpeciesAliasXmlParser(elements, model2);
+ Species alias2 = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals(protein.getActivity(), alias2.getActivity());
+ assertEquals(protein.getElementId(), alias2.getElementId());
+ assertEquals(protein.getFontSize(), alias2.getFontSize(), 1e-6);
+ assertEquals(protein.getHeight(), alias2.getHeight(), 1e-6);
+ assertEquals(protein.getWidth(), alias2.getWidth(), 1e-6);
+ assertEquals(protein.getX(), alias2.getX(), 1e-6);
+ assertEquals(protein.getY(), alias2.getY(), 1e-6);
+ assertEquals(protein.getCompartment().getElementId(), alias2.getCompartment().getElementId());
+ assertEquals("Alias state label different", protein.getStateLabel(), alias2.getStateLabel());
+ assertEquals("Alias state prefix different", protein.getStatePrefix(), alias2.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Species createProtein() {
+ GenericProtein protein = new GenericProtein("id");
+ protein.setActivity(true);
+ protein.setFontSize(4);
+ protein.setHeight(10);
+ protein.setWidth(20);
+ protein.setX(30);
+ protein.setY(40);
+ protein.setStateLabel("xxx");
+ protein.setStatePrefix("yyy");
+ return protein;
+ }
+
+ @Test
+ public void testToXmlAliasWithStateNode() throws Exception {
+ try {
+ Model model = createStubModel();
+ Species protein = createProtein();
+ protein.setState("sssstate");
+ protein.setCompartment(model.getCompartments().iterator().next());
+ elements.addElement(new CellDesignerGenericProtein(elements.getElementId(protein)));
+ String xmlString = parser.toXml(protein);
+
+ Species alias2 = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+
+ assertEquals("Alias state label different", protein.getStateLabel(), alias2.getStateLabel());
+ assertEquals("Alias state prefix different", protein.getStatePrefix(), alias2.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasWithStateNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_with_state.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(alias);
+ assertEquals("test", alias.getStateLabel());
+ assertEquals("free input", alias.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseXmlAliasWithoutStateNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/species_alias_without_state.xml");
+ Species alias = parser.parseXmlAlias(xmlString);
+ assertEquals(0, getWarnings().size());
+ assertNotNull(alias);
+ assertNull(alias.getStateLabel());
+ assertNull(alias.getStatePrefix());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown species for alias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode2() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias2.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:speciesAlias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode3() throws Exception {
+ try {
+ String xmlString = readFile("testFiles/invalid/species_alias3.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("No view in Alias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode4() throws Exception {
+ try {
+ parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xmlString = readFile("testFiles/invalid/species_alias4.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("CompartmentAlias does not exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode5() throws Exception {
+ try {
+ parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xmlString = readFile("testFiles/invalid/species_alias5.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (InvalidXmlSchemaException e) {
+ assertTrue(e.getMessage().contains("ComplexAlias does not exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidXmlAliasNode6() throws Exception {
+ try {
+ parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xmlString = readFile("testFiles/invalid/species_alias6.xml");
+ parser.parseXmlAlias(xmlString);
+ fail("Exception expected");
+ } catch (NotImplementedException e) {
+ assertTrue(e.getMessage().contains("Unkown alias state"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testToXmlWithUnknownCompartment() throws Exception {
+ try {
+ Model model = Mockito.mock(ModelFullIndexed.class);
+ ModelData md = new ModelData();
+ md.setModel(model);
+
+ Compartment ca2 = new Compartment(testCompartmentAliasId2);
+ ca2.setElementId(testCompartmentAliasId2);
+ ca2.setX(6);
+ ca2.setY(6);
+ ca2.setWidth(190);
+ ca2.setHeight(190);
+
+ Compartment ca = new Compartment(testCompartmentAliasId);
+ ca.setElementId(testCompartmentAliasId);
+ ca.setX(5);
+ ca.setY(5);
+ ca.setWidth(200);
+ ca.setHeight(200);
+
+ List<Compartment> list = new ArrayList<>();
+ list.add(ca);
+ list.add(ca2);
+
+ // ensure that we return list (firts bigger compartment, then smaller)
+ when(model.getCompartments()).thenReturn(list);
+ when(model.getModelData()).thenReturn(md);
+
+ Species alias = new Complex(testAliasId);
+ alias.setX(10);
+ alias.setY(10);
+ alias.setWidth(100);
+ alias.setHeight(100);
+ alias.setModel(model);
+ alias.setActivity(true);
+
+ elements.addElement(new CellDesignerComplexSpecies(testSpeciesId));
+ model.addElement(alias);
+ SpeciesAliasXmlParser parser = new SpeciesAliasXmlParser(elements, model);
+
+ String xml = parser.toXml(alias);
+
+ assertTrue(xml.contains(testAliasId));
+ assertTrue(xml.contains(testCompartmentAliasId2));
+ assertTrue(xml.contains("<celldesigner:activity>active</celldesigner:activity>"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
index 6b027c8e0f..5828d1ac3e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
@@ -452,7 +452,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
try {
// test situation when createProperTypeReaction returns reaction of
// unknown type
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
return result;
}
@@ -483,7 +483,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
}
}
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
return new NewReactionType(result);
}
@@ -507,7 +507,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoProductReaction encounter
// reaction with two many base reactants
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addReactant(new Reactant());
@@ -533,7 +533,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoProductReaction encounter
// reaction with two many base products
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addProduct(new Product());
@@ -567,7 +567,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
}
}
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
return new NewReactionType(result);
}
@@ -590,7 +590,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoReactantReaction encounter
// reaction with two many base reactants
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addReactant(new Reactant());
@@ -615,7 +615,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createOperatorsForTwoReactantReaction encounter
// reaction with two many base products
- ReactionFromXml parser = new ReactionFromXml(false) {
+ ReactionFromXml parser = new ReactionFromXml(null, false) {
Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
Reaction r = super.createProperTypeReaction(type, result);
r.addProduct(new Product());
@@ -637,7 +637,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
@Test
public void testParseInvalidEditPointsString() throws Exception {
try {
- ReactionFromXml parser = new ReactionFromXml(false);
+ ReactionFromXml parser = new ReactionFromXml(null, false);
parser.parseEditPointsString("1");
fail("Exception expected");
@@ -652,7 +652,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
@Test
public void testParseInvalidEditPointsString2() throws Exception {
try {
- ReactionFromXml parser = new ReactionFromXml(false);
+ ReactionFromXml parser = new ReactionFromXml(null, false);
parser.parseEditPointsString("1,Infinity");
fail("Exception expected");
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
index f9f7d55853..a62c5c340e 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionParserTests.java
@@ -1856,4 +1856,16 @@ public class ReactionParserTests extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testKinetcsWithCompartment() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions/kinetics_with_compartment.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertNotNull(reaction.getKinetics());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-CellDesigner/testFiles/reactions/kinetics_with_compartment.xml b/converter-CellDesigner/testFiles/reactions/kinetics_with_compartment.xml
new file mode 100644
index 0000000000..5bc746a066
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reactions/kinetics_with_compartment.xml
@@ -0,0 +1,189 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="46.0" y="105.0" w="413.0" h="201.0"/>
+<celldesigner:namePoint x="244.0" y="270.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="67.0" y="151.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="21.0" y="46.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="296.0" y="174.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="250.0" y="69.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false" fast="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<kineticLaw metaid="CDMT00003">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<divide/>
+<apply>
+<times/>
+<ci> c1 </ci>
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</apply>
+<cn type="integer"> 2 </cn>
+</apply>
+</math>
+</kineticLaw>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 190f1c84fb..8b7657a831 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -351,7 +351,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* Parse and set font size.
*
* @param string
- * text representing font sizee
+ * text representing font size
* @see fontSize
*/
public void setFontSize(String string) {
--
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