From c6fc262f0a63b65576b1e1bd578ed5dfa34ecadf Mon Sep 17 00:00:00 2001
From: sherzinger <sascha.herzinger@uni.lu>
Date: Tue, 19 Feb 2019 08:33:20 +0100
Subject: [PATCH] refactored another class to no longer extend XmlParser
---
.../species/SpeciesSbmlParser.java | 65 ++++++++++---------
1 file changed, 33 insertions(+), 32 deletions(-)
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index b4fd701dbc..e26f5c94e1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
+import lcsb.mapviewer.common.XmlParser;
import org.apache.log4j.Logger;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -128,7 +129,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
// itself
continue;
} else {
- throw new InvalidXmlSchemaException("[" + getNodeAttr("id", spieciesNode)
+ throw new InvalidXmlSchemaException("[" + XmlParser.getNodeAttr("id", spieciesNode)
+ "]\tUnknown element of celldesigner:extension " + node.getNodeName());
}
}
@@ -143,33 +144,33 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
CellDesignerSpecies<?> species = result.getRight();
if (positionToCompartment != null) {
- PositionToCompartment position = PositionToCompartment.getByString(getNodeValue(positionToCompartment));
+ PositionToCompartment position = PositionToCompartment.getByString(XmlParser.getNodeValue(positionToCompartment));
if (position == null) {
- throw new InvalidXmlSchemaException("Unknown position on compartment: " + getNodeValue(positionToCompartment));
+ throw new InvalidXmlSchemaException("Unknown position on compartment: " + XmlParser.getNodeValue(positionToCompartment));
}
species.setPositionToCompartment(position);
}
// we ignore metaid - it's useless and obstruct data model
- // species.setMetaId(getNodeAttr("metaid", spieciesNode));
- species.setElementId(getNodeAttr("id", spieciesNode));
- species.setName(decodeName(getNodeAttr("name", spieciesNode)));
- species.setInitialAmount(getNodeAttr("initialAmount", spieciesNode));
- String substanceUnits = getNodeAttr("substanceUnits", spieciesNode);
+ // species.setMetaId(XmlParser.getNodeAttr("metaid", spieciesNode));
+ species.setElementId(XmlParser.getNodeAttr("id", spieciesNode));
+ species.setName(decodeName(XmlParser.getNodeAttr("name", spieciesNode)));
+ species.setInitialAmount(XmlParser.getNodeAttr("initialAmount", spieciesNode));
+ String substanceUnits = XmlParser.getNodeAttr("substanceUnits", spieciesNode);
if (substanceUnits != null && !substanceUnits.isEmpty()) {
species.setSubstanceUnits(SbmlUnitType.valueOf(substanceUnits.toUpperCase()));
}
- species.setInitialAmount(getNodeAttr("initialAmount", spieciesNode));
- species.setInitialConcentration(getNodeAttr("initialConcentration", spieciesNode));
+ species.setInitialAmount(XmlParser.getNodeAttr("initialAmount", spieciesNode));
+ species.setInitialConcentration(XmlParser.getNodeAttr("initialConcentration", spieciesNode));
if (species.getInitialAmount() == null && species.getInitialConcentration() == null) {
species.setInitialConcentration(0.0);
}
- species.setCharge(getNodeAttr("charge", spieciesNode));
- species.setOnlySubstanceUnits(getNodeAttr("hasOnlySubstanceUnits", spieciesNode));
- species.setBoundaryCondition(getNodeAttr("boundaryCondition", spieciesNode));
- species.setConstant(getNodeAttr("constant", spieciesNode));
+ species.setCharge(XmlParser.getNodeAttr("charge", spieciesNode));
+ species.setOnlySubstanceUnits(XmlParser.getNodeAttr("hasOnlySubstanceUnits", spieciesNode));
+ species.setBoundaryCondition(XmlParser.getNodeAttr("boundaryCondition", spieciesNode));
+ species.setConstant(XmlParser.getNodeAttr("constant", spieciesNode));
- CellDesignerCompartment compartment = elements.getElementByElementId(getNodeAttr("compartment", spieciesNode));
+ CellDesignerCompartment compartment = elements.getElementByElementId(XmlParser.getNodeAttr("compartment", spieciesNode));
if (compartment != null) {
species.setParent(compartment);
}
@@ -190,7 +191,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
public String toXml(Species species) {
StringBuilder builder = new StringBuilder();
StringBuilder attributesBuilder = new StringBuilder();
- attributesBuilder.append(" name=\"" + escapeXml(encodeName(species.getName())) + "\"");
+ attributesBuilder.append(" name=\"" + XmlParser.escapeXml(encodeName(species.getName())) + "\"");
attributesBuilder.append(" id=\"" + elements.getElementId(species) + "\"");
attributesBuilder.append(" metaid=\"" + elements.getElementId(species) + "\"");
if (species.getInitialAmount() != null) {
@@ -305,7 +306,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
SpeciesState state = new SpeciesState(species);
sb.append(speciesStateToXml(state));
- sb.append("<celldesigner:name>" + escapeXml(encodeName(species.getName())) + "</celldesigner:name>\n");
+ sb.append("<celldesigner:name>" + XmlParser.escapeXml(encodeName(species.getName())) + "</celldesigner:name>\n");
Boolean hypothetical = species.getHypothetical();
if (hypothetical != null) {
@@ -362,11 +363,11 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
public Pair<String, CellDesignerSpecies<?>> parseSpeciesIdentity(Node rootNode) throws InvalidXmlSchemaException {
NodeList nodes = rootNode.getChildNodes();
CellDesignerSpecies<?> result = new CellDesignerSpecies<Species>();
- Node classNode = getNode("celldesigner:class", nodes);
+ Node classNode = XmlParser.getNode("celldesigner:class", nodes);
if (classNode == null) {
throw new InvalidXmlSchemaException("Species node in Sbml model doesn't contain node \"celldesigner:class\".");
} else {
- String value = getNodeValue(classNode);
+ String value = XmlParser.getNodeValue(classNode);
SpeciesMapping mapping = SpeciesMapping.getMappingByString(value);
if (mapping != null) {
result = mapping.createSpecies(result);
@@ -382,34 +383,34 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
continue;
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:proteinReference")) {
if (result instanceof CellDesignerProtein) {
- identifier = getNodeValue(node);
+ identifier = XmlParser.getNodeValue(node);
} else {
throw new InvalidXmlSchemaException(
"Wrong class type for protein reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:geneReference")) {
if (result instanceof CellDesignerGene) {
- identifier = getNodeValue(node);
+ identifier = XmlParser.getNodeValue(node);
} else {
throw new InvalidXmlSchemaException("Wrong class type for gene reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:rnaReference")) {
if (result instanceof CellDesignerRna) {
- identifier = getNodeValue(node);
+ identifier = XmlParser.getNodeValue(node);
} else {
throw new InvalidXmlSchemaException("Wrong class type for rna reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:antisensernaReference")) {
if (result instanceof CellDesignerAntisenseRna) {
- identifier = getNodeValue(node);
+ identifier = XmlParser.getNodeValue(node);
} else {
throw new InvalidXmlSchemaException(
"Wrong class type for antisense rna reference: " + result.getClass().getName());
}
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:hypothetical")) {
- result.setHypothetical(getNodeValue(node));
+ result.setHypothetical(XmlParser.getNodeValue(node));
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:name")) {
- result.setName(decodeName(getNodeValue(node)));
+ result.setName(decodeName(XmlParser.getNodeValue(node)));
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:state")) {
SpeciesState state = parseXmlSpeciesState(node);
processStateDataInSpecies(result, state);
@@ -509,14 +510,14 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
Node node = nodes.item(x);
if (node.getNodeType() == Node.ELEMENT_NODE) {
if (node.getNodeName().equalsIgnoreCase("celldesigner:homodimer")) {
- result.setHomodimer(getNodeValue(node));
+ result.setHomodimer(XmlParser.getNodeValue(node));
} else if (node.getNodeName().equalsIgnoreCase("celldesigner:listOfStructuralStates")) {
NodeList structureNodeList = node.getChildNodes();
for (int y = 0; y < structureNodeList.getLength(); y++) {
Node structureNode = structureNodeList.item(y);
if (structureNode.getNodeType() == Node.ELEMENT_NODE) {
if (structureNode.getNodeName().equalsIgnoreCase("celldesigner:structuralState")) {
- String state = getNodeAttr("structuralState", structureNode);
+ String state = XmlParser.getNodeAttr("structuralState", structureNode);
result.setStructuralState(state);
} else {
throw new InvalidXmlSchemaException(
@@ -563,8 +564,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
*/
private CellDesignerModificationResidue getSpeciesModification(Node rootNode) throws InvalidXmlSchemaException {
CellDesignerModificationResidue modification = new CellDesignerModificationResidue();
- modification.setIdModificationResidue(getNodeAttr("residue", rootNode));
- String state = getNodeAttr("state", rootNode);
+ modification.setIdModificationResidue(XmlParser.getNodeAttr("residue", rootNode));
+ String state = XmlParser.getNodeAttr("state", rootNode);
if (state != null) {
ModificationState mState = ModificationState.getByName(state);
if (mState == null) {
@@ -573,9 +574,9 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
}
modification.setState(mState);
}
- modification.setName(getNodeAttr("name", rootNode));
- modification.setSize(getNodeAttr("size", rootNode));
- modification.setAngle(getNodeAttr("pos", rootNode));
+ modification.setName(XmlParser.getNodeAttr("name", rootNode));
+ modification.setSize(XmlParser.getNodeAttr("size", rootNode));
+ modification.setAngle(XmlParser.getNodeAttr("pos", rootNode));
NodeList list = rootNode.getChildNodes();
for (int y = 0; y < list.getLength(); y++) {
Node node = list.item(y);
--
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