From 9af1f06e5027c87af9f5f16ee7bf31a518c5d7b4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 5 Oct 2018 10:47:06 +0200
Subject: [PATCH] parsing results/products returns object instead of injecting
them
---
.../reaction/ReactionFromXml.java | 276 +++++++++---------
1 file changed, 138 insertions(+), 138 deletions(-)
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 5d9907db3a..32b7f91967 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
@@ -357,146 +357,151 @@ public class ReactionFromXml extends XmlParser {
*
*/
private Reaction parseReactionExtension(Reaction result, Node node, Model model) throws ReactionParserException {
- NodeList extensionNodes = node.getChildNodes();
- LineProperties line = null;
- ConnectScheme connectScheme = null;
- EditPoints points = null;
- Node reactantsLinkNode = null;
- Node productsLinkNode = null;
- Node modifiersLinkNode = null;
- Node gateMembers = null;
- String type = null;
- for (int y = 0; y < extensionNodes.getLength(); y++) {
- Node nodeReaction = extensionNodes.item(y);
- if (nodeReaction.getNodeType() == Node.ELEMENT_NODE) {
- if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:reactionType")) {
- type = getNodeValue(nodeReaction);
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseReactants")) {
- NodeList reactantsNodes = nodeReaction.getChildNodes();
- for (int z = 0; z < reactantsNodes.getLength(); z++) {
- Node reactantNode = reactantsNodes.item(z);
- if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
- if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseReactant")) {
- parseBaseReactant(result, reactantNode, model);
- } else {
- throw new ReactionParserException(
- "Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
+ try {
+ NodeList extensionNodes = node.getChildNodes();
+ LineProperties line = null;
+ ConnectScheme connectScheme = null;
+ EditPoints points = null;
+ Node reactantsLinkNode = null;
+ Node productsLinkNode = null;
+ Node modifiersLinkNode = null;
+ Node gateMembers = null;
+ String type = null;
+ for (int y = 0; y < extensionNodes.getLength(); y++) {
+ Node nodeReaction = extensionNodes.item(y);
+ if (nodeReaction.getNodeType() == Node.ELEMENT_NODE) {
+ if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:reactionType")) {
+ type = getNodeValue(nodeReaction);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseReactants")) {
+ NodeList reactantsNodes = nodeReaction.getChildNodes();
+ for (int z = 0; z < reactantsNodes.getLength(); z++) {
+ Node reactantNode = reactantsNodes.item(z);
+ if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseReactant")) {
+ result.addReactant(parseBaseReactant(reactantNode, model));
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
+ }
}
}
- }
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseProducts")) {
- NodeList reactantsNodes = nodeReaction.getChildNodes();
- for (int z = 0; z < reactantsNodes.getLength(); z++) {
- Node reactantNode = reactantsNodes.item(z);
- if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
- if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseProduct")) {
- parseBaseProduct(model, result, reactantNode);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:baseProducts: " + node.getNodeName(),
- result);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:baseProducts")) {
+ NodeList reactantsNodes = nodeReaction.getChildNodes();
+ for (int z = 0; z < reactantsNodes.getLength(); z++) {
+ Node reactantNode = reactantsNodes.item(z);
+ if (reactantNode.getNodeType() == Node.ELEMENT_NODE) {
+ if (reactantNode.getNodeName().equalsIgnoreCase("celldesigner:baseProduct")) {
+ result.addProduct(parseBaseProduct(model, reactantNode));
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of celldesigner:baseProducts: " + node.getNodeName(), result);
+ }
}
}
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ line = getLineProperties(nodeReaction);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ try {
+ connectScheme = parseConnectScheme(nodeReaction);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(result, e);
+ }
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfReactantLinks")) {
+ reactantsLinkNode = nodeReaction;
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfProductLinks")) {
+ productsLinkNode = nodeReaction;
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfModification")) {
+ modifiersLinkNode = nodeReaction;
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
+ points = parseEditPoints(nodeReaction);
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:name")) {
+ result.setName(getNodeValue(nodeReaction));
+ } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfGateMember")) {
+ gateMembers = nodeReaction;
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of reaction/celldesigner:extension: " + nodeReaction.getNodeName(), result);
}
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- line = getLineProperties(nodeReaction);
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- try {
- connectScheme = parseConnectScheme(nodeReaction);
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(result, e);
- }
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfReactantLinks")) {
- reactantsLinkNode = nodeReaction;
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfProductLinks")) {
- productsLinkNode = nodeReaction;
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfModification")) {
- modifiersLinkNode = nodeReaction;
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
- points = parseEditPoints(nodeReaction);
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:name")) {
- result.setName(getNodeValue(nodeReaction));
- } else if (nodeReaction.getNodeName().equalsIgnoreCase("celldesigner:listOfGateMember")) {
- gateMembers = nodeReaction;
- } else {
- throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:extension: " + nodeReaction.getNodeName(), result);
}
}
- }
- if (gateMembers != null) {
- try {
- points = gateMembersToPoints(gateMembers);
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(result, e);
+ if (gateMembers != null) {
+ try {
+ points = gateMembersToPoints(gateMembers);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(result, e);
+ }
+ }
+ result = createProperTypeReaction(type, result);
+ if (connectScheme == null) {
+ throw new ReactionParserException("No connectScheme node", result);
+ }
+ if (points == null) {
+ points = new EditPoints();
+ }
+ if (result instanceof SimpleReactionInterface) {
+ createLinesForSimpleReaction(result, points, connectScheme);
+ } else if (result instanceof TwoReactantReactionInterface) {
+ createLinesForTwoReactantReaction(result, points, gateMembers != null);
+ createOperatorsForTwoReactantReaction(result, gateMembers);
+
+ } else if (result instanceof TwoProductReactionInterface) {
+ createLinesForTwoProductReaction(result, points);
+ createOperatorsForTwoProductReaction(result);
+ } else {
+ throw new ReactionParserException(
+ "Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
+ }
+ if (reactantsLinkNode != null) {
+ parseReactantLinks(result, reactantsLinkNode, model);
+ }
+ if (productsLinkNode != null) {
+ parseProductLinks(result, productsLinkNode, model);
}
- }
- result = createProperTypeReaction(type, result);
- if (connectScheme == null) {
- throw new ReactionParserException("No connectScheme node", result);
- }
- if (points == null) {
- points = new EditPoints();
- }
- if (result instanceof SimpleReactionInterface) {
- createLinesForSimpleReaction(result, points, connectScheme);
- } else if (result instanceof TwoReactantReactionInterface) {
- createLinesForTwoReactantReaction(result, points, gateMembers != null);
- createOperatorsForTwoReactantReaction(result, gateMembers);
-
- } else if (result instanceof TwoProductReactionInterface) {
- createLinesForTwoProductReaction(result, points);
- createOperatorsForTwoProductReaction(result);
- } else {
- throw new ReactionParserException(
- "Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
- }
- if (reactantsLinkNode != null) {
- parseReactantLinks(result, reactantsLinkNode, model);
- }
- if (productsLinkNode != null) {
- parseProductLinks(result, productsLinkNode, model);
- }
- // create operators
- createOperators(result);
+ // create operators
+ createOperators(result);
- // now try to create modifiers (we must have set fixed layout data for the
- // core of the reaction)
- if (modifiersLinkNode != null) {
- parseReactionModification(result, modifiersLinkNode, model);
- }
- for (int i = 0; i < result.getModifiers().size(); i++) {
- Modifier modifier = result.getModifiers().get(i);
- if (modifier.getElement() == null) {
- List<Modifier> modifiers = new ArrayList<Modifier>();
- modifiers.add(modifier);
- for (Modifier modifier2 : result.getModifiers()) {
- if (modifierParentOperator.get(modifier2) == modifier) {
- modifiers.add(modifier2);
+ // now try to create modifiers (we must have set fixed layout data for the
+ // core of the reaction)
+ if (modifiersLinkNode != null) {
+ parseReactionModification(result, modifiersLinkNode, model);
+ }
+ for (int i = 0; i < result.getModifiers().size(); i++) {
+ Modifier modifier = result.getModifiers().get(i);
+ if (modifier.getElement() == null) {
+ List<Modifier> modifiers = new ArrayList<Modifier>();
+ modifiers.add(modifier);
+ for (Modifier modifier2 : result.getModifiers()) {
+ if (modifierParentOperator.get(modifier2) == modifier) {
+ modifiers.add(modifier2);
+ }
}
+ computeLineForModification(result, modifiers);
+ createOperatorFromModifiers(result, modifiers);
+ result.removeModifier(modifier);
+ i--;
+ } else if (modifier.getLine() == null) {
+ createLineForModifier(result, modifier);
}
- computeLineForModification(result, modifiers);
- createOperatorFromModifiers(result, modifiers);
- result.removeModifier(modifier);
- i--;
- } else if (modifier.getLine() == null) {
- createLineForModifier(result, modifier);
}
- }
- if (line != null) {
- for (AbstractNode rNode : result.getNodes()) {
- rNode.getLine().setWidth(line.getWidth());
- rNode.getLine().setColor(line.getColor());
+ if (line != null) {
+ for (AbstractNode rNode : result.getNodes()) {
+ rNode.getLine().setWidth(line.getWidth());
+ rNode.getLine().setColor(line.getColor());
+ }
}
- }
- if (result.isReversible()) {
- for (Reactant reactant : result.getReactants()) {
- reactant.getLine().getBeginAtd().setArrowType(result.getProducts().get(0).getLine().getEndAtd().getArrowType());
+ if (result.isReversible()) {
+ for (Reactant reactant : result.getReactants()) {
+ reactant.getLine().getBeginAtd()
+ .setArrowType(result.getProducts().get(0).getLine().getEndAtd().getArrowType());
+ }
}
- }
- return result;
+ return result;
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(e.getMessage(), result, e);
+ }
}
/**
@@ -1688,8 +1693,6 @@ public class ReactionFromXml extends XmlParser {
* PArses baseReactant node from CellDEsigenr xml node and adds it into
* reaction.
*
- * @param result
- * reaction that is processed
* @param reactantNode
* xml node to parse
* @param model
@@ -1698,14 +1701,13 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseBaseReactant(Reaction result, Node reactantNode, Model model) throws ReactionParserException {
+ private Reactant parseBaseReactant(Node reactantNode, Model model) throws InvalidXmlSchemaException {
String aliasId = getNodeAttr("alias", reactantNode);
Species alias = model.getElementByElementId(aliasId);
if (alias == null) {
- throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
+ throw new InvalidXmlSchemaException("Alias with id=" + aliasId + " doesn't exist.");
}
Reactant reactant = new Reactant(alias);
- result.addReactant(reactant);
NodeList nodes = reactantNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
@@ -1713,19 +1715,17 @@ public class ReactionFromXml extends XmlParser {
if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
anchorsByNodes.put(reactant, CellDesignerAnchor.valueOf(getNodeAttr("position", node)));
} else {
- throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName(), result);
+ throw new InvalidXmlSchemaException(
+ "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
}
}
-
}
+ return reactant;
}
/**
* Parses baseProduct node from CellDEsigenr xml node and adds it into reaction.
*
- * @param result
- * reaction that is processed
* @param reactantNode
* xml node to parse
* @param model
@@ -1734,14 +1734,13 @@ public class ReactionFromXml extends XmlParser {
* thrown when xml node contains data that is not supported by xml
* schema
*/
- private void parseBaseProduct(Model model, Reaction result, Node reactantNode) throws ReactionParserException {
+ private Product parseBaseProduct(Model model, Node reactantNode) throws InvalidXmlSchemaException {
String aliasId = getNodeAttr("alias", reactantNode);
Species species = model.getElementByElementId(aliasId);
if (species == null) {
- throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
+ throw new InvalidXmlSchemaException("Alias with id=" + aliasId + " doesn't exist.");
}
Product product = new Product(species);
- result.addProduct(product);
NodeList nodes = reactantNode.getChildNodes();
for (int x = 0; x < nodes.getLength(); x++) {
Node node = nodes.item(x);
@@ -1749,11 +1748,12 @@ public class ReactionFromXml extends XmlParser {
if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
anchorsByNodes.put(product, CellDesignerAnchor.valueOf(getNodeAttr("position", node)));
} else {
- throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:baseProduct: " + node.getNodeName(), result);
+ throw new InvalidXmlSchemaException(
+ "Unknown element of reaction/celldesigner:baseProduct: " + node.getNodeName());
}
}
}
+ return product;
}
--
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