diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java index c27fb104955f21e8a7adb31bac586a1c2dfb20fe..53197344f5d124d645fcea1fd30b4ad967282c86 100644 --- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java +++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java @@ -4,6 +4,7 @@ import java.util.ArrayList; import java.util.Collection; import java.util.List; +import lcsb.mapviewer.common.XmlParser; import org.apache.log4j.Logger; import org.sbml.jsbml.ListOf; import org.sbml.jsbml.Model; @@ -24,10 +25,10 @@ public class SbmlFunctionParser extends SbmlBioEntityParser { try { SbmlFunction result = new SbmlFunction(unitDefinition.getId()); result.setName(unitDefinition.getName()); - Node node = super.getXmlDocumentFromString(unitDefinition.getMath().toMathML()); - Node mathDefinition = getNode("math", node); + Node node = XmlParser.getXmlDocumentFromString(unitDefinition.getMath().toMathML()); + Node mathDefinition = XmlParser.getNode("math", node); String definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" - + nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "") + "</math>"; + + XmlParser.nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", "") + "</math>"; result.setDefinition(definition); result.setArguments(parseArgumentsFromMath(mathDefinition, result.getFunctionId())); return result; @@ -39,13 +40,13 @@ public class SbmlFunctionParser extends SbmlBioEntityParser { private List<String> parseArgumentsFromMath(Node mathDefinition, String functionId) throws InvalidXmlSchemaException { List<String> result = new ArrayList<>(); - Node lambdaDefinition = getNode("lambda", mathDefinition); + Node lambdaDefinition = XmlParser.getNode("lambda", mathDefinition); if (lambdaDefinition == null) { throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain valid MathML lambda node"); } - List<Node> variables = super.getNodes("bvar", lambdaDefinition.getChildNodes()); + List<Node> variables = XmlParser.getNodes("bvar", lambdaDefinition.getChildNodes()); for (Node node : variables) { - result.add(getNodeValue(getNode("ci", node)).trim()); + result.add(XmlParser.getNodeValue(XmlParser.getNode("ci", node)).trim()); } return result; } diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java index 609ef982edc86da2a0048c713979bc281d17142f..2a794130e0a026ca886772b93532109ae86d343a 100644 --- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java +++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java @@ -10,6 +10,7 @@ import java.util.HashMap; import java.util.List; import java.util.Map; +import lcsb.mapviewer.common.XmlParser; import org.apache.log4j.Logger; import org.sbml.jsbml.ASTNode; import org.sbml.jsbml.KineticLaw; @@ -130,9 +131,9 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb } try { - Node node = super.getXmlDocumentFromString(kinetics.getDefinition()); - for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", node)) { - String id = super.getNodeValue(ciNode).trim(); + Node node = XmlParser.getXmlDocumentFromString(kinetics.getDefinition()); + for (Node ciNode : XmlParser.getAllNotNecessirellyDirectChild("ci", node)) { + String id = XmlParser.getNodeValue(ciNode).trim(); Element element = getMinervaModel().getElementByElementId(id); if (element != null) { String sbmlId = null; @@ -145,7 +146,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb ciNode.setTextContent(sbmlId); } } - String definition = super.nodeToString(node); + String definition = XmlParser.nodeToString(node); definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", ""); definition = definition.replace("<math>", "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">"); result.setMath(ASTNode.parseMathML(definition)); diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java index 43560808a8f36e53eaf9a91faa749e62a7b5d93d..bf6aac35adaa11a56cd4726e487d216883d42858 100644 --- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java +++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java @@ -11,6 +11,7 @@ import java.util.List; import java.util.Map; import java.util.Set; +import lcsb.mapviewer.common.XmlParser; import org.apache.log4j.Logger; import org.sbml.jsbml.KineticLaw; import org.sbml.jsbml.ListOf; @@ -569,9 +570,9 @@ public class SbmlReactionParser extends SbmlBioEntityParser { result.addParameters(parameterParser.parseList((Collection<LocalParameter>) kineticLaw.getListOfLocalParameters())); try { - Node node = super.getXmlDocumentFromString(result.getDefinition()); + Node node = XmlParser.getXmlDocumentFromString(result.getDefinition()); Set<SbmlArgument> elementsUsedInKinetics = new HashSet<>(); - for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", node)) { + for (Node ciNode : XmlParser.getAllNotNecessirellyDirectChild("ci", node)) { List<String> attributesToRemove = new ArrayList<>(); for (int y = 0; y < ciNode.getAttributes().getLength(); y++) { Node attr = ciNode.getAttributes().item(y); @@ -582,7 +583,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser { logger.warn("Kinetics attribute not supported: " + attributeName); } - String id = super.getNodeValue(ciNode).trim(); + String id = XmlParser.getNodeValue(ciNode).trim(); SbmlArgument element = getMinervaModel().getElementByElementId(id); if (element == null) { element = result.getParameterById(id); @@ -603,7 +604,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser { } } result.addArguments(elementsUsedInKinetics); - result.setDefinition(super.nodeToString(node)); + result.setDefinition(XmlParser.nodeToString(node)); } catch (InvalidXmlSchemaException e) { throw new InvalidInputDataExecption(e); }