diff --git a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
index 451deb265f68c530d378655394d234e67e1cec2a..d7ac52a2907e84754893e53ebc8f4148760bbd47 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/XmlParser.java
@@ -41,325 +41,338 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
*
*/
public class XmlParser {
- /**
- * Base of the hex representation.
- */
- private static final int HEX_BASE = 16;
+ /**
+ * Base of the hex representation.
+ */
+ private static final int HEX_BASE = 16;
- /**
- * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder}
- * objects that will manipulate xml nodes.
- */
- private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
+ /**
+ * {@link DocumentBuilderFactory} used to create {@link DocumentBuilder} objects
+ * that will manipulate xml nodes.
+ */
+ private static DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(XmlParser.class.getName());
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(XmlParser.class.getName());
- /**
- * DOM document builder used for xml transformations.
- */
- private DocumentBuilder db;
+ /**
+ * DOM document builder used for xml transformations.
+ */
+ private DocumentBuilder db;
- /**
- * Default constructor that prevents from instatiation of the class and
- * initializes fields.
- */
- protected XmlParser() {
- try {
- db = documentBuilderFactory.newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidStateException("Problem with xml parser");
- }
+ /**
+ * Default constructor that prevents from instatiation of the class and
+ * initializes fields.
+ */
+ protected XmlParser() {
+ try {
+ db = documentBuilderFactory.newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidStateException("Problem with xml parser");
+ }
- }
+ }
- /**
- * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If
- * node could not be found then null is returned.
- *
- * @param tagName
- * name of node to look for
- * @param nodes
- * list of nodes
- * @return node from nodes list with the tagName name, <b>null</b> if such
- * node doesn't exist
- */
- protected Node getNode(final String tagName, final NodeList nodes) {
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- return node;
- }
- }
- }
- return null;
- }
+ /**
+ * Method returns the node of xml nodelist 'nodes' with 'tagName' name. If node
+ * could not be found then null is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param nodes
+ * list of nodes
+ * @return node from nodes list with the tagName name, <b>null</b> if such node
+ * doesn't exist
+ */
+ protected Node getNode(final String tagName, final NodeList nodes) {
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ return node;
+ }
+ }
+ }
+ return null;
+ }
- /**
- * Method returns the child node of xml 'parentNode' with 'tagName' name. If
- * node could not be found then null is returned.
- *
- * @param tagName
- * name of node to look for
- * @param parentNode
- * parent node
- * @return node from nodes list with the tagName name, <b>null</b> if such
- * node doesn't exist
- */
- protected Node getNode(final String tagName, final Node parentNode) {
- return getNode(tagName, parentNode.getChildNodes());
- }
+ /**
+ * Method returns the child node of xml 'parentNode' with 'tagName' name. If
+ * node could not be found then null is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param parentNode
+ * parent node
+ * @return node from nodes list with the tagName name, <b>null</b> if such node
+ * doesn't exist
+ */
+ protected Node getNode(final String tagName, final Node parentNode) {
+ return getNode(tagName, parentNode.getChildNodes());
+ }
- /**
- * Method returns list of nodes with 'tagName' name. If node could not be
- * found then empty list is returned.
- *
- * @param tagName
- * name of node to look for
- * @param nodes
- * list of input nodes
- * @return list of nodes with 'tagName' name
- */
- protected List<Node> getNodes(final String tagName, final NodeList nodes) {
- List<Node> result = new ArrayList<Node>();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeName().equalsIgnoreCase(tagName)) {
- result.add(node);
- }
- }
- return result;
- }
+ /**
+ * Method returns list of nodes with 'tagName' name. If node could not be found
+ * then empty list is returned.
+ *
+ * @param tagName
+ * name of node to look for
+ * @param nodes
+ * list of input nodes
+ * @return list of nodes with 'tagName' name
+ */
+ protected List<Node> getNodes(final String tagName, final NodeList nodes) {
+ List<Node> result = new ArrayList<Node>();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ result.add(node);
+ }
+ }
+ return result;
+ }
- /**
- * Method returns the value of node attribute. If attribute could not be found
- * then "" is returned.
- *
- * @param attrName
- * name of the attribute to look for
- * @param node
- * a node
- * @return the value of node attribute, empty string("") if attribute doesn't
- * exist
- */
- protected String getNodeAttr(final String attrName, final Node node) {
- NamedNodeMap attrs = node.getAttributes();
- for (int y = 0; y < attrs.getLength(); y++) {
- Node attr = attrs.item(y);
- if (attr.getNodeName().equalsIgnoreCase(attrName)) {
- return attr.getNodeValue();
- }
- }
- return "";
- }
+ /**
+ * Method returns the value of node attribute. If attribute could not be found
+ * then "" is returned.
+ *
+ * @param attrName
+ * name of the attribute to look for
+ * @param node
+ * a node
+ * @return the value of node attribute, empty string("") if attribute doesn't
+ * exist
+ */
+ protected String getNodeAttr(final String attrName, final Node node) {
+ NamedNodeMap attrs = node.getAttributes();
+ for (int y = 0; y < attrs.getLength(); y++) {
+ Node attr = attrs.item(y);
+ if (attr.getNodeName().equalsIgnoreCase(attrName)) {
+ return attr.getNodeValue();
+ }
+ }
+ return "";
+ }
- /**
- * Method returns the text value of node. If text could not be found then ""
- * is returned.
- *
- * @param node
- * a node
- * @return the text value of node or empty string ("") if the text could be
- * found.
- */
- protected String getNodeValue(final Node node) {
- if (node == null) {
- return "";
- }
- NodeList childNodes = node.getChildNodes();
- for (int x = 0; x < childNodes.getLength(); x++) {
- Node data = childNodes.item(x);
- if (data.getNodeType() == Node.TEXT_NODE) {
- return data.getNodeValue();
- }
- }
- return "";
- }
+ /**
+ * Method returns the text value of node. If text could not be found then "" is
+ * returned.
+ *
+ * @param node
+ * a node
+ * @return the text value of node or empty string ("") if the text could be
+ * found.
+ */
+ protected String getNodeValue(final Node node) {
+ if (node == null) {
+ return "";
+ }
+ NodeList childNodes = node.getChildNodes();
+ for (int x = 0; x < childNodes.getLength(); x++) {
+ Node data = childNodes.item(x);
+ if (data.getNodeType() == Node.TEXT_NODE) {
+ return data.getNodeValue();
+ }
+ }
+ return "";
+ }
- /**
- * Method returns the xml Document from input source given as a parameter.
- *
- * @param stream
- * input stream with xml document
- * @return Document node for the input stream
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
- try {
- synchronized (db) { // DocumentBuilder cannot parse few objects at the
- // same time
- return db.parse(stream);
- }
- } catch (SAXException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser", e);
- } catch (IOException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser", e);
- }
- }
+ /**
+ * Method returns the xml Document from input source given as a parameter.
+ *
+ * @param stream
+ * input stream with xml document
+ * @return Document node for the input stream
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ protected Document getXmlDocumentFromInputSource(final InputSource stream) throws InvalidXmlSchemaException {
+ try {
+ synchronized (db) { // DocumentBuilder cannot parse few objects at the
+ // same time
+ return db.parse(stream);
+ }
+ } catch (SAXException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser", e);
+ } catch (IOException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser", e);
+ }
+ }
- /**
- * Method returns the xml Document from text given as a source.
- *
- * @param text
- * string representing xml document
- * @return Document for the xml document given in the input
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- try {
- return getXmlDocumentFromInputSource(is);
- } catch (NullPointerException e) {
- logger.error("Problem with input xml: " + text);
- throw new InvalidXmlSchemaException(e);
- }
- }
+ /**
+ * Method returns the xml Document from text given as a source.
+ *
+ * @param text
+ * string representing xml document
+ * @return Document for the xml document given in the input
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ protected Document getXmlDocumentFromString(final String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ try {
+ return getXmlDocumentFromInputSource(is);
+ } catch (NullPointerException e) {
+ logger.error("Problem with input xml: " + text);
+ throw new InvalidXmlSchemaException(e);
+ }
+ }
- /**
- * Transforms node into string xml format.
- *
- * @param node
- * node that should be transformed into xml string
- * @return string representation of the xml node
- */
- protected String nodeToString(final Node node) {
- return nodeToString(node, false);
- }
+ /**
+ * Transforms node into string xml format.
+ *
+ * @param node
+ * node that should be transformed into xml string
+ * @return string representation of the xml node
+ */
+ protected String nodeToString(final Node node) {
+ return nodeToString(node, false);
+ }
- /**
- * Transforms node into string xml format.
- *
- * @param node
- * node that should be transformed into xml string
- * @param includeHeadNode
- * should the top level node exist in the output
- * @return string representation of the xml node
- */
- protected String nodeToString(final Node node, final boolean includeHeadNode) {
- if (node == null) {
- return null;
- }
- StringWriter sw = new StringWriter();
- try {
- Transformer t = TransformerFactory.newInstance().newTransformer();
- t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- t.setOutputProperty(OutputKeys.INDENT, "yes");
- t.setOutputProperty(OutputKeys.METHOD, "xml");
+ /**
+ * Transforms node into string xml format.
+ *
+ * @param node
+ * node that should be transformed into xml string
+ * @param includeHeadNode
+ * should the top level node exist in the output
+ * @return string representation of the xml node
+ */
+ protected String nodeToString(final Node node, final boolean includeHeadNode) {
+ if (node == null) {
+ return null;
+ }
+ StringWriter sw = new StringWriter();
+ try {
+ Transformer t = TransformerFactory.newInstance().newTransformer();
+ t.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ t.setOutputProperty(OutputKeys.INDENT, "yes");
+ t.setOutputProperty(OutputKeys.METHOD, "xml");
- NodeList list = node.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node element = list.item(i);
- t.transform(new DOMSource(element), new StreamResult(sw));
- }
- } catch (TransformerException te) {
- logger.debug("nodeToString Transformer Exception");
- }
- if (includeHeadNode) {
- return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
- }
- return sw.toString();
- }
+ NodeList list = node.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node element = list.item(i);
+ t.transform(new DOMSource(element), new StreamResult(sw));
+ }
+ } catch (TransformerException te) {
+ logger.debug("nodeToString Transformer Exception");
+ }
+ if (includeHeadNode) {
+ return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
+ }
+ return sw.toString();
+ }
- /**
- * This method transform color encoded in string (CellDesigner format) into
- * Color.
- *
- * @param color
- * string representing color
- * @return Color object for the fiven string
- */
- protected Color stringToColor(final String color) {
- try {
- String alpha = color.substring(0, 2);
- Color tmp = new Color(hexToInteger(color.substring(2)));
- return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
- } catch (Exception e) {
- throw new InvalidArgumentException("Invalid color string: " + color);
- }
- }
+ /**
+ * This method transform color encoded in string (CellDesigner format) into
+ * Color.
+ *
+ * @param color
+ * string representing color
+ * @return Color object for the fiven string
+ */
+ protected Color stringToColor(final String color) {
+ try {
+ String alpha = color.substring(0, 2);
+ Color tmp = new Color(hexToInteger(color.substring(2)));
+ return new Color(tmp.getRed(), tmp.getGreen(), tmp.getBlue(), hexToInteger(alpha));
+ } catch (Exception e) {
+ throw new InvalidArgumentException("Invalid color string: " + color);
+ }
+ }
- /**
- * Transforms hex string into Integer.
- *
- * @param hexString
- * string representation in hex base
- * @return Integer value of the hex string
- */
- private Integer hexToInteger(String hexString) {
- return Integer.valueOf(hexString, HEX_BASE);
- }
+ /**
+ * Transforms hex string into Integer.
+ *
+ * @param hexString
+ * string representation in hex base
+ * @return Integer value of the hex string
+ */
+ private Integer hexToInteger(String hexString) {
+ return Integer.valueOf(hexString, HEX_BASE);
+ }
- /**
- * Transforms Color object into string representing this color in RGB.
- *
- * @param color
- * color that should be converted into string
- * @return hex string representation of the color
- */
- protected String colorToString(final Color color) {
- return String.format("%08X", color.getRGB());
- }
+ /**
+ * Transforms Color object into string representing this color in RGB.
+ *
+ * @param color
+ * color that should be converted into string
+ * @return hex string representation of the color
+ */
+ protected String colorToString(final Color color) {
+ return String.format("%08X", color.getRGB());
+ }
- /**
- * Method that reads file and transforms it into a string.
- *
- * @param fileName
- * path to a file
- * @return string containing data from the file (default coding is used)
- * @throws IOException
- * thrown when there are some problems with a file
- */
- protected String fileToString(final String fileName) throws IOException {
- BufferedReader reader = new BufferedReader(new FileReader(fileName));
- String line = null;
- StringBuilder stringBuilder = new StringBuilder();
- String ls = System.getProperty("line.separator");
+ /**
+ * Method that reads file and transforms it into a string.
+ *
+ * @param fileName
+ * path to a file
+ * @return string containing data from the file (default coding is used)
+ * @throws IOException
+ * thrown when there are some problems with a file
+ */
+ protected String fileToString(final String fileName) throws IOException {
+ BufferedReader reader = new BufferedReader(new FileReader(fileName));
+ String line = null;
+ StringBuilder stringBuilder = new StringBuilder();
+ String ls = System.getProperty("line.separator");
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- reader.close();
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ reader.close();
- return stringBuilder.toString();
- }
+ return stringBuilder.toString();
+ }
- /**
- * Method that reads all data from inputstream and transform it into a string.
- * UTF-8 coding is used.
- *
- * @param inputStream
- * stream from which we read data
- * @return string representing all data from input stream
- * @throws IOException
- * thrown if there are some problems with input stream
- */
- protected String inputStreamToString(final InputStream inputStream) throws IOException {
- StringWriter writer = new StringWriter();
- IOUtils.copy(inputStream, writer, "UTF-8");
- String result = writer.toString();
- return result;
- }
+ /**
+ * Method that reads all data from inputstream and transform it into a string.
+ * UTF-8 coding is used.
+ *
+ * @param inputStream
+ * stream from which we read data
+ * @return string representing all data from input stream
+ * @throws IOException
+ * thrown if there are some problems with input stream
+ */
+ protected String inputStreamToString(final InputStream inputStream) throws IOException {
+ StringWriter writer = new StringWriter();
+ IOUtils.copy(inputStream, writer, "UTF-8");
+ String result = writer.toString();
+ return result;
+ }
- /**
- * Method that encode string into a string that can be used in xml file.
- *
- * @param string
- * string to be escaped
- * @return escaped string, ready to be used in xml
- */
- protected String escapeXml(final String string) {
- if (string == null) {
- return null;
- }
- // quite expensive
- return StringEscapeUtils.escapeXml(string).replaceAll("\n", " ").replace("\r", " ");
- }
+ /**
+ * Method that encode string into a string that can be used in xml file.
+ *
+ * @param string
+ * string to be escaped
+ * @return escaped string, ready to be used in xml
+ */
+ protected String escapeXml(final String string) {
+ if (string == null) {
+ return null;
+ }
+ // quite expensive
+ return StringEscapeUtils.escapeXml(string).replaceAll("\n", " ").replace("\r", " ");
+ }
+
+ public List<Node> getAllNotNecessirellyDirectChild(String tagName, Node root) {
+ List<Node> result = new ArrayList<>();
+ for (int x = 0; x < root.getChildNodes().getLength(); x++) {
+ Node node = root.getChildNodes().item(x);
+ if (node.getNodeName().equalsIgnoreCase(tagName)) {
+ result.add(node);
+ } else {
+ result.addAll(getAllNotNecessirellyDirectChild(tagName, node));
+ }
+ }
+ return result;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..ef91803efe11a4e8d5195a23f5cbc7c61ea6cca6
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParser.java
@@ -0,0 +1,64 @@
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+
+public class KineticsXmlParser extends XmlParser {
+ Logger logger = Logger.getLogger(KineticsXmlParser.class);
+
+ ParameterCollectionXmlParser parameterParser;
+
+ Model model;
+
+ public KineticsXmlParser(Model model) {
+ this.model = model;
+ parameterParser = new ParameterCollectionXmlParser(model);
+ }
+
+ public SbmlKinetics parseKinetics(Node kineticsNode, Map<String, Element> elements) throws InvalidXmlSchemaException {
+ SbmlKinetics result = new SbmlKinetics();
+ Node mathNode = super.getNode("math", kineticsNode);
+ if (mathNode == null) {
+ throw new InvalidXmlSchemaException("kineticLaw node doesn't have math subnode");
+ }
+
+ Node parametersNode = super.getNode("listOfParameters", kineticsNode);
+ if (parametersNode != null) {
+ result.addParameters(parameterParser.parseXmlParameterCollection(parametersNode));
+ }
+
+ Set<SbmlArgument> elementsUsedInKinetics = new HashSet<>();
+ for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", mathNode)) {
+ String id = super.getNodeValue(ciNode).trim();
+ SbmlArgument element = elements.get(id);
+ if (element == null) {
+ element = result.getParameterById(id);
+ }
+ if (element == null) {
+ element = model.getParameterById(id);
+ }
+ if (element == null) {
+ element = model.getFunctionById(id);
+ }
+ if (element == null) {
+ throw new InvalidXmlSchemaException("Unknown symbol in kinetics: " + id);
+ }
+ elementsUsedInKinetics.add(element);
+ }
+ result.addArguments(elementsUsedInKinetics);
+
+ return result;
+ }
+}
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 2b428bfdb9d9b35db0e3be6aa438bec9f5dae9f6..735682c06731c429303b449c70524311958d42c3 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
@@ -70,1568 +70,1617 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class ReactionFromXml extends XmlParser {
- /**
- * Reactant lines in cell designer ends in the 2/5 of the center line.
- */
- private static final double REACTANT_END_RATIO = 0.4;
-
- /**
- * Product lines in cell designer starts in the 3/5 of the center line.
- */
- private static final double PRODUCT_START_RATIO = 0.6;
-
- /**
- * Stores information about {@link CellDesignerAnchor} for a node.
- */
- private Map<ReactionNode, CellDesignerAnchor> anchorsByNodes = new HashMap<ReactionNode, CellDesignerAnchor>();
-
- /**
- * Stores information about operator type that should be used for a modifier
- * node.
- */
- private Map<ReactionNode, String> typeByModifier = new HashMap<ReactionNode, String>();
-
- /**
- * Stores information to which point on the central rectangle modifier should
- * be connected.
- */
- private Map<ReactionNode, String> lineTypeByModifier = new HashMap<ReactionNode, String>();
-
- /**
- * Stores information about list of points that create line describing
- * modifier.
- */
- private Map<ReactionNode, List<Point2D>> pointsByModifier = new HashMap<ReactionNode, List<Point2D>>();
-
- /**
- * Helps to determine if the key Modifier should be treates as part of
- * NodeOperator (value in the map).
- */
- private Map<Modifier, Modifier> modifierParentOperator = new HashMap<Modifier, Modifier>();
-
- /**
- * Identifies central line segment in {@link TwoProductReactionInterface} and
- * {@link TwoReactantReactionInterface} reactions.
- */
- private Map<ReactionNode, Integer> indexByComplexReaction = new HashMap<ReactionNode, Integer>();
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ReactionXmlParser.class.getName());
-
- /**
- * Xml parser used for processing notes into structurized data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Helper object used for manipulation on the point coorinates in CellDesigner
- * format.
- */
- private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
-
- /**
- * Should sbgn standard be used.
- */
- private boolean sbgn;
-
- /**
- * Default constructor.
- *
- * @param sbgn
- * Should the converter use sbgn standard
- */
- public ReactionFromXml(boolean sbgn) {
- this.sbgn = sbgn;
- }
-
- /**
- * Returns {@link Reaction} object from CellDesigner xml node.
- *
- * @param reactionNode
- * xml node
- * @param model
- * model where the reaction is placed
- * @return reactin from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when reactionNode is invalid xml
- */
- public Reaction getReaction(Node reactionNode, Model model) throws ReactionParserException {
- Reaction result = new Reaction();
- // we ignore metaid - it's useless and obstruct data model
- // result.setMetaId(getNodeAttr("metaid", reactionNode));
- result.setIdReaction(getNodeAttr("id", reactionNode));
- result.setName(getNodeAttr("name", reactionNode));
- // by default this value is true...
- result.setReversible(!(getNodeAttr("reversible", reactionNode).equalsIgnoreCase("false")));
-
- NodeList nodes = reactionNode.getChildNodes();
- Node annotationNode = null;
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("annotation")) {
- annotationNode = node;
- } else if (node.getNodeName().equalsIgnoreCase("listOfReactants")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfProducts")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("listOfModifiers")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("notes")) {
- rap.processNotes(rap.getNotes(node), result);
- } else if (node.getNodeName().equalsIgnoreCase("kineticLaw")) {
- // this definitelly needs to be improved!!!
- // up to now we didn't do anything about kinetics
-
- Node kineticLaw = node;
- Node mathNode = getNode("math", kineticLaw.getChildNodes());
- if (mathNode == null) {
- throw new ReactionParserException("kineticLaw node doesn't have math subnode", result);
- }
- String xmlns = getNodeAttr("xmlns", mathNode);
- if (!xmlns.equals("http://www.w3.org/1998/Math/MathML")) {
- throw new ReactionParserException("invalid value in math xmlns attrib: " + xmlns, result);
- }
- result.setKineticLaw(true);
- } else {
- throw new ReactionParserException("Unknown element of reaction: " + node.getNodeName(), result);
- }
- }
- }
- if (annotationNode != null) {
- result = parseReactionAnnotation(annotationNode, result, model);
- } else {
- throw new ReactionParserException("No annotation node in reaction", result);
- }
-
- return result;
- }
-
- /**
- * Parses reaction annotation node and update reaction.
- *
- * @param annotationNode
- * xml node
- * @param result
- * reaction to update
- * @param model
- * model where reaction is placed
- * @return updated reaction
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when annotationNode is invalid xml
- */
- private Reaction parseReactionAnnotation(Node annotationNode, Reaction result, Model model) throws ReactionParserException {
- NodeList nodes = annotationNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
- result = parseReactionExtension(result, node, model);
- } else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
- try {
- XmlAnnotationParser xmlParser = new XmlAnnotationParser();
- result.addMiriamData(xmlParser.parseRdfNode(nodes));
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException("Problem with parsing RDF", result, e);
- }
- } else {
- throw new ReactionParserException("Unknown element of reaction/annotation: " + node.getNodeName(), result);
- }
- }
- }
- return result;
- }
-
- /**
- * Parses CellDesigner extension to sbml reaction node and updates reaction.
- *
- * @param result
- * reaction to update
- * @param node
- * xml node
- * @param model
- * model where reaction is placed
- * @return updated reaction
- * @throws ReactionParserException
- * thrown when the xml is invalid and reason is more specific
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- *
- */
- 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);
- }
- }
- }
- } 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: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);
- }
- }
- 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);
-
- // 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);
- }
- }
-
- 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());
- }
- }
-
- return result;
- }
-
- /**
- * Creates reaction with a new type.
- *
- * @param type
- * CellDesigner type of a reaction
- * @param result
- * initial data
- * @return reaction with a new type
- * @throws UnknownReactionClassException
- * thrown when type is invalid
- */
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- ReactionLineData rdl = ReactionLineData.getByCellDesignerString(type);
- if (rdl == null) {
- throw new UnknownReactionClassException("Unknown CellDesigner class type: " + type + ".", type, result.getIdReaction());
- }
- return rdl.createReaction(result);
- }
-
- /**
- * Creates CellDesigner {@link EditPoints} structure for gate members node.
- *
- * @param gateMembers
- * xml node
- * @return {@link EditPoints} structure representing line information for the
- * xml node
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private EditPoints gateMembersToPoints(Node gateMembers) throws InvalidXmlSchemaException {
- Node lastMember = null;
- EditPoints result = new EditPoints();
- Integer num0 = null;
- Integer num1 = null;
- Integer num2 = null;
- for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
- Node child = gateMembers.getChildNodes().item(i);
- if (child.getNodeType() == Node.ELEMENT_NODE) {
-
- if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
- String type = getNodeAttr("type", child);
- if (type.startsWith(ReactionLineData.BOOLEAN_LOGIC_GATE.getCellDesignerString())) {
- lastMember = child;
- } else {
- String pointsString = getNodeAttr("editPoints", child);
- List<Point2D> points = parseEditPointsString(pointsString);
- if (num0 == null) {
- num0 = points.size();
- } else if (num1 == null) {
- num1 = points.size();
- } else {
- throw new InvalidXmlSchemaException("Too many gate members");
- }
- result.getPoints().addAll(points);
- }
- } else {
- throw new InvalidXmlSchemaException("Unknown node type: " + child.getNodeName());
- }
- }
- }
- if (lastMember == null) {
- throw new InvalidXmlSchemaException("Missing gate member connecting members");
- } else {
- String pointsString = getNodeAttr("editPoints", lastMember);
- List<Point2D> points = parseEditPointsString(pointsString);
- num2 = points.size() - 1;
- result.getPoints().addAll(points);
- }
- result.setNum0(num0);
- result.setNum1(num1);
- result.setNum2(num2);
- return result;
- }
-
- /**
- * Creates line information for the modifier.
- *
- * @param reaction
- * reaction where modifier is placed
- * @param modifier
- * modifier to update
- */
- private void createLineForModifier(Reaction reaction, Modifier modifier) {
- Element element = modifier.getElement();
- CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
- Point2D startPoint = converter.getPointCoordinates(element, anchorsByNodes.get(modifier));
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
-
- Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(), lineTypeByModifier.get(modifier));
- PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p, pointsByModifier.get(modifier));
-
- startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
- line.setStartPoint(startPoint);
- modifier.setLine(line);
- modifierTypeUtils.updateLineEndPoint(modifier);
- }
-
- /**
- * Creates operators for CellDesigner reaction that belongs to
- * {@link TwoProductReactionInterface}.
- *
- * @param result
- * reaction to be updated
- * @throws ReactionParserException
- * thrown when there is a problem with creating operators (input
- * data is invalid)
- */
- private void createOperatorsForTwoProductReaction(Reaction result) throws ReactionParserException {
- int inputs = 0;
- NodeOperator operator = null;
- if (result.getClass() == DissociationReaction.class) {
- operator = new DissociationOperator();
- } else if (result.getClass() == TruncationReaction.class) {
- operator = new TruncationOperator();
- } else {
- throw new ReactionParserException("Invalid reaction type", result);
- }
- for (AbstractNode node : result.getNodes()) {
- if (node.getClass() == Product.class) {
- operator.addOutput(node);
- } else if (node.getClass() == Reactant.class) {
- inputs++;
- if (inputs > 1) {
- throw new ReactionParserException("Reaction has more than one reactant", result);
- }
- }
- }
- if (operator.getOutputs().size() > 2) {
- throw new ReactionParserException("Too many products: " + operator.getOutputs().size(), result);
- }
-
- // and now we have to modify lines
-
- Reactant reactant = result.getReactants().get(0);
- Integer index = indexByComplexReaction.get(reactant);
-
- Point2D p1, p2;
-
- p1 = reactant.getLine().getPoints().get(index);
- p2 = reactant.getLine().getPoints().get(index + 1);
-
- p1 = new Point2D.Double(p1.getX(), p1.getY());
- p2 = new Point2D.Double(p2.getX(), p2.getY());
-
- Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- operator.setLine(reactant.getLine().getSubline(0, index + 1));
- operator.getLine().addPoint(p);
-
- p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
-
- reactant.setLine(reactant.getLine().getSubline(index + 1, reactant.getLine().getPoints().size()).reverse());
- reactant.getLine().getPoints().add(p);
-
- reactant.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- operator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- result.addNode(operator);
- }
-
- /**
- * Creates general input/output operators for the model.
- *
- * @param result
- * reaction to be updated
- */
- private void createOperators(Reaction result) {
- // central line points
- Point2D p1 = result.getReactants().get(0).getLine().getPoints().get(result.getReactants().get(0).getLine().getPoints().size() - 2);
- Point2D p2 = result.getProducts().get(0).getLine().getPoints().get(1);
- Point2D tmp = result.getProducts().get(0).getLine().getPoints().get(0);
- Point2D productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
-
- // where the line from reactants ends
- tmp = result.getReactants().get(0).getLine().getPoints().get(result.getReactants().get(0).getLine().getPoints().size() - 1);
- Point2D reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
-
- Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
- Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
- for (NodeOperator operator : result.getOperators()) {
- toExclude.addAll(operator.getInputs());
- if (operator.isReactantOperator()) {
- toInclude.add(operator);
- // if we have operator in input then central line changes
- p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
- reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
- }
- if (operator.isProductOperator()) {
- // if we have operator in output then central line changes
- p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
- productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
- }
- }
-
- double dx = p2.getX() - p1.getX();
- double dy = p2.getY() - p1.getY();
-
- Point2D reactantAndOperatorBeginPoint = new Point2D.Double(p1.getX() + dx * REACTANT_END_RATIO, p1.getY() + dy * REACTANT_END_RATIO);
-
- PolylineData ld = new PolylineData(reactantAndOperatorBeginPoint, reactantAndOperatorEndPoint);
-
- LineType lineType = null;
- Set<AbstractNode> nodes = new LinkedHashSet<AbstractNode>();
- for (Reactant reactant : result.getReactants()) {
- if (!toExclude.contains(reactant)) {
- nodes.add(reactant);
- if (lineType == null) {
- lineType = reactant.getLine().getType();
- }
- }
- }
- nodes.addAll(toInclude);
- nodes.removeAll(toExclude);
-
- // add an operator only when the number of input nodes is greater than one
- if (nodes.size() > 1) {
- AndOperator inputOperator = new AndOperator();
- inputOperator.setLine(ld);
- inputOperator.addInputs(nodes);
- for (Reactant reactant : result.getReactants()) {
- if (!toExclude.contains(reactant)) {
- reactant.getLine().getEndPoint().setLocation(reactantAndOperatorBeginPoint.getX(), reactantAndOperatorBeginPoint.getY());
- }
- }
- if (lineType != null) {
- inputOperator.getLine().setType(lineType);
- }
- result.addNode(inputOperator);
- }
-
- // and now we try to handle with output operators
-
- toExclude = new HashSet<AbstractNode>();
- toInclude = new HashSet<AbstractNode>();
- for (NodeOperator nOperator : result.getOperators()) {
- toExclude.addAll(nOperator.getOutputs());
- if (nOperator.isProductOperator()) {
- toInclude.add(nOperator);
- }
- }
-
- Point2D productSplitOperatorEndPoint = new Point2D.Double(p1.getX() + dx * PRODUCT_START_RATIO, p1.getY() + dy * PRODUCT_START_RATIO);
-
- ld = new PolylineData(productSplitOperatorEndPoint, productSplitOperatorBeginPoint);
-
- lineType = null;
- nodes = new LinkedHashSet<AbstractNode>();
- for (Product product : result.getProducts()) {
- if (!toExclude.contains(product)) {
- nodes.add(product);
- if (lineType == null) {
- lineType = product.getLine().getType();
- }
- }
- }
- nodes.addAll(toInclude);
- nodes.removeAll(toExclude);
- if (nodes.size() > 1) {
- SplitOperator outputOperator = new SplitOperator();
- outputOperator.setLine(ld);
- outputOperator.addOutputs(nodes);
- for (Product product : result.getProducts()) {
- if (!toExclude.contains(product)) {
- // outputOperator.addOutput(product);
- product.getLine().getPoints().get(0).setLocation(productSplitOperatorEndPoint.getX(), productSplitOperatorEndPoint.getY());
- }
- }
- if (lineType != null) {
- outputOperator.getLine().setType(lineType);
- }
- result.addNode(outputOperator);
- }
- }
-
- /**
- * Creates operators in modifiers.
- *
- * @param reaction
- * reaction to update
- * @param modifiers
- * list of modifiers that must be put into operators
- */
- private void createOperatorFromModifiers(Reaction reaction, List<Modifier> modifiers) {
- OperatorTypeUtils otu = new OperatorTypeUtils();
- String type = typeByModifier.get(modifiers.get(0));
- NodeOperator operator = otu.createModifierForStringType(type);
-
- operator.setLine(modifiers.get(0).getLine());
-
- for (int i = 1; i < modifiers.size(); i++) {
- operator.addInput(modifiers.get(i));
- }
-
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- modifierTypeUtils.updateLineEndPoint(operator);
- reaction.addNode(operator);
- }
-
- /**
- * Creates operators for CellDesigner reaction that belongs to
- * {@link TwoReactantReactionInterface}.
- *
- * @param result
- * reaction to be updated
- * @param gateMembers
- * node representing line information for the operator
- * @throws ReactionParserException
- * thrown when the xml is invalid
- */
- private void createOperatorsForTwoReactantReaction(Reaction result, Node gateMembers) throws ReactionParserException {
- NodeOperator andOperator = null;
- if (result instanceof HeterodimerAssociationReaction) {
- andOperator = new AssociationOperator();
- } else if (result instanceof BooleanLogicGateReaction) {
- andOperator = new AndOperator();
- } else {
- throw new ReactionParserException("Unknown class type with two reactants", result);
- }
- int outputs = 0;
- for (AbstractNode node : result.getNodes()) {
- if (node.getClass() == Reactant.class) {
- andOperator.addInput(node);
- } else if (node.getClass() == Product.class) {
- outputs++;
- if (outputs > 1) {
- throw new ReactionParserException("Reaction has more than one product", result);
- }
- }
- }
- if (andOperator.getInputs().size() > 2) {
- throw new ReactionParserException("Too many reactants.", result);
- }
-
- // and now we have to modify lines
-
- Product product = result.getProducts().get(0);
- Integer index = indexByComplexReaction.get(product);
- if (index != null) {
- Point2D p1, p2;
-
- p1 = product.getLine().getPoints().get(index);
- p2 = product.getLine().getPoints().get(index + 1);
-
- p1 = new Point2D.Double(p1.getX(), p1.getY());
- p2 = new Point2D.Double(p2.getX(), p2.getY());
-
- Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- andOperator.setLine(product.getLine().getSubline(0, index + 1));
- andOperator.getLine().addPoint(p);
- andOperator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
-
- product.setLine(product.getLine().getSubline(index, product.getLine().getPoints().size()));
- product.getLine().getPoints().set(0, p);
- product.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
-
- result.addNode(andOperator);
- } else {
- NodeOperator operator = null;
- Set<String> undefinedTypes = new HashSet<String>();
- for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
- Node child = gateMembers.getChildNodes().item(i);
- if (child.getNodeType() == Node.ELEMENT_NODE) {
-
- if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
- String type = getNodeAttr("type", child);
-
- if (type.equalsIgnoreCase(OperatorType.AND_OPERATOR_STRING.getStringName())) {
- operator = new AndOperator();
- } else if (type.equalsIgnoreCase(OperatorType.OR_OPERATOR_STRING.getStringName())) {
- operator = new OrOperator();
- } else if (type.equalsIgnoreCase(OperatorType.NAND_OPERATOR_STRING.getStringName())) {
- operator = new NandOperator();
- } else if (type.equalsIgnoreCase(OperatorType.UNKNOWN_OPERATOR_STRING.getStringName())) {
- operator = new UnknownOperator();
- } else {
- undefinedTypes.add(type);
- }
- }
- }
- }
- if (operator == null) {
- String types = "";
- for (String string : undefinedTypes) {
- types += string + ", ";
- }
- throw new ReactionParserException("Couldn't find type of BOOLEAN_LOGIC_GATE. Unknown types identified: " + types, result);
- }
-
- operator.addInputs(andOperator.getInputs());
- operator.addOutput(product);
-
- // empty line
- PolylineData line = new PolylineData();
- line.addPoint(product.getLine().getBeginPoint());
- line.addPoint(product.getLine().getBeginPoint());
-
- operator.setLine(line);
- result.addNode(operator);
- }
-
- }
-
- /**
- * Creates lines for reaction that belongs to
- * {@link TwoProductReactionInterface}.
- *
- * @param reaction
- * reaction to update
- * @param points
- * information about points
- */
- private void createLinesForTwoProductReaction(Reaction reaction, EditPoints points) {
- Point2D p = points.getPoints().get(points.size() - 1);
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
- Reactant reactant = reaction.getReactants().get(0);
-
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
- CellDesignerAliasConverter product1Converter = new CellDesignerAliasConverter(product1.getElement(), sbgn);
- CellDesignerAliasConverter product2Converter = new CellDesignerAliasConverter(product2.getElement(), sbgn);
-
- Point2D p1 = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
- Point2D p2 = product1Converter.getPointCoordinates(product1.getElement(), anchorsByNodes.get(product1));
- Point2D p3 = product2Converter.getPointCoordinates(product2.getElement(), anchorsByNodes.get(product2));
-
- Point2D centerPoint = pointTransformation
- .getCoordinatesInNormalBase(product1.getElement().getCenter(), product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
-
- int startId0 = 0;
- int num0 = points.getNum0();
- int startId1 = num0;
- int num1 = num0 + points.getNum1();
- int startId2 = num1;
- int num2 = num1 + points.getNum2();
-
- ArrayList<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
- ArrayList<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
- ArrayList<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
-
- PolylineData product1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
- PolylineData product2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
-
- PolylineData reactantLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
-
- p1 = product2Converter.getAnchorPointCoordinates(product2.getElement(), anchorsByNodes.get(product2), product2Line.reverse());
- product2Line.setEndPoint(p1);
-
- p1 = product1Converter.getAnchorPointCoordinates(product1.getElement(), anchorsByNodes.get(product1), product1Line.reverse());
- product1Line.setEndPoint(p1);
-
- p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), reactantLine.reverse());
- reactantLine.setEndPoint(p1);
-
- product2Line.getEndAtd().setArrowType(ArrowType.FULL);
- product1Line.getEndAtd().setArrowType(ArrowType.FULL);
- product1.setLine(product1Line);
- product2.setLine(product2Line);
- reactant.setLine(reactantLine);
-
- indexByComplexReaction.put(reactant, points.getIndex());
-
- }
-
- /**
- * Creates lines for reaction that belongs to
- * {@link TwoReactantReactionInterface}.
- *
- * @param reaction
- * reaction to update
- * @param points
- * information about points
- * @param hasGateMemebers
- * does the reaction has gate members
- * @throws ReactionParserException
- * thrown when data for reaction is invalid
- */
- private void createLinesForTwoReactantReaction(Reaction reaction, EditPoints points, boolean hasGateMemebers) throws ReactionParserException {
- Point2D p = points.getPoints().get(points.size() - 1);
- Product product = reaction.getProducts().get(0);
- Reactant reactant1 = reaction.getReactants().get(0);
- Reactant reactant2 = reaction.getReactants().get(1);
- CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
- CellDesignerAliasConverter reactantConverter1 = new CellDesignerAliasConverter(reactant1.getElement(), sbgn);
- CellDesignerAliasConverter reactantConverter2 = new CellDesignerAliasConverter(reactant2.getElement(), sbgn);
- Point2D p1 = reactantConverter1.getPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1));
- Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2));
- Point2D p3 = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
-
- Element alias1 = reactant1.getElement();
- Element alias2 = reactant2.getElement();
- Element alias3 = product.getElement();
-
- Point2D pointA = alias2.getCenter();
- Point2D pointC = alias1.getCenter();
- Point2D pointB = alias3.getCenter();
- Point2D pointP = p;
- Point2D centerPoint = null;
- if (!hasGateMemebers) {
- centerPoint = pointTransformation.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
- } else {
- centerPoint = pointP;
- }
-
- int startId0 = 0;
- int num0 = points.getNum0();
- int startId1 = num0;
- int num1 = num0 + points.getNum1();
- int startId2 = num1;
- int num2 = num1 + points.getNum2();
-
- List<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
- List<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
- List<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
-
- PolylineData reactant1Line = null;
- PolylineData reactant2Line = null;
- if (!hasGateMemebers) {
- reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
- reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
- } else {
- reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(p1, centerPoint, linePoints1);
- reactant1Line = reactant1Line.reverse();
-
- reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(p2, centerPoint, linePoints2);
- reactant2Line = reactant2Line.reverse();
- }
-
- PolylineData productLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
-
- p1 = reactantConverter1.getAnchorPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1), reactant1Line.reverse());
- reactant1Line.setEndPoint(p1);
- reactant1Line = reactant1Line.reverse();
-
- p1 = reactantConverter2.getAnchorPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2), reactant2Line.reverse());
- reactant2Line.setEndPoint(p1);
- reactant2Line = reactant2Line.reverse();
-
- p1 = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product), productLine.reverse());
- productLine.setEndPoint(p1);
- if (hasGateMemebers) {
- productLine.getEndAtd().setArrowType(ArrowType.OPEN);
- }
-
- product.setLine(productLine);
- reactant1.setLine(reactant1Line);
- reactant2.setLine(reactant2Line);
-
- indexByComplexReaction.put(product, points.getIndex());
- }
-
- /**
- * Creates lines for reaction that belongs to {@link SimpleReactionInterface}
- * (only one standard product and one standard reactant).
- *
- * @param reaction
- * reaction to update
- * @param editPoints
- * information about points
- * @param scheme
- * some additional information about the line
- */
- private void createLinesForSimpleReaction(Reaction reaction, EditPoints editPoints, ConnectScheme scheme) {
- Product product = reaction.getProducts().get(0);
- Reactant reactant = reaction.getReactants().get(0);
- CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
-
- Point2D endPoint = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
- Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
-
- PolylineData ld = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint, editPoints.getPoints());
-
- // first place where the index of rectangle is kept
- Integer index = editPoints.getIndex();
-
- // second place where index of rectangle is kept
- if (index == null) {
- index = scheme.getConnectIndex();
- if (index != null) {
- // but...
- // direction of the index is reversed...
- index = ld.getPoints().size() - index - 2;
- }
- }
- // but sometimes there is no information about index...
- if (index == null) {
- index = 0;
- }
- startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), ld);
- endPoint = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product), ld.reverse());
- ld.getPoints().set(0, startPoint);
- ld.getPoints().set(ld.getPoints().size() - 1, endPoint);
-
- PolylineData line = new PolylineData(ld);
-
- PolylineData reactantLine = line.getSubline(0, ld.getPoints().size() - index - 1);
- PolylineData productLine = line.getSubline(ld.getPoints().size() - index - 2, ld.getPoints().size());
-
- Point2D p1 = ld.getPoints().get(ld.getPoints().size() - index - 2);
- Point2D p2 = ld.getPoints().get(ld.getPoints().size() - index - 1);
- Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- reactantLine.getPoints().add(p);
- reactantLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
- productLine.getPoints().set(0, p);
- productLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
-
- productLine.getEndAtd().setArrowType(ArrowType.FULL);
-
- reactant.setLine(reactantLine);
- product.setLine(productLine);
-
- ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
- reactantLine.setType(rld.getLineType());
- productLine.setType(rld.getLineType());
- productLine.getEndAtd().setArrowType(rld.getProductArrowType());
- productLine.trimEnd(rld.getProductLineTrim());
- }
-
- /**
- * Prepares {@link EditPoints} structure from xml node.
- *
- * @param rootNode
- * xml node
- * @return {@link EditPoints} object containing CellDesigner line data
- */
- private EditPoints parseEditPoints(Node rootNode) {
- EditPoints result = new EditPoints();
- String num0 = getNodeAttr("num0", rootNode);
- String num1 = getNodeAttr("num1", rootNode);
- String num2 = getNodeAttr("num2", rootNode);
- if (!num0.equals("")) {
- result.setNum0(Integer.parseInt(num0));
- }
- if (!num1.equals("")) {
- result.setNum1(Integer.parseInt(num1));
- }
- if (!num2.equals("")) {
- result.setNum2(Integer.parseInt(num2));
- }
- String index = getNodeAttr("tShapeIndex", rootNode);
- if (!index.equals("")) {
- result.setIndex(Integer.parseInt(index));
- }
-
- String pointsString = getNodeValue(rootNode);
- result.setPoints(parseEditPointsString(pointsString));
- return result;
- }
-
- /**
- * Parses CellDesigner point by point string.
- *
- * @param pointsString
- * String containing points
- * @return list of points
- */
- ArrayList<Point2D> parseEditPointsString(String pointsString) {
- ArrayList<Point2D> points2 = new ArrayList<Point2D>();
- if (pointsString.isEmpty()) {
- return points2;
- }
- String[] points = pointsString.trim().split(" ");
- for (String string : points) {
- String[] p = string.split(",");
- if (p.length != 2) {
- throw new InvalidArgumentException("Invalid editPoint string: " + string);
- } else {
- double posX = Double.parseDouble(p[0]);
- double posY = Double.parseDouble(p[1]);
- Point2D point = new Point2D.Double(posX, posY);
- if (!pointTransformation.isValidPoint(point)) {
- throw new InvalidArgumentException("Invalid point parsed from input string: " + string + ". Result point: " + point);
- }
- points2.add(point);
- }
- }
- return points2;
- }
-
- /**
- * Parses xml node with reactantLink nodes and creates reactants in the
- * reaction.
- *
- * @param result
- * reaction to be updated
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseReactantLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
- NodeList list = rootNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:reactantLink")) {
- Reactant newReactant = getReactantLink(node, model, result);
- result.addReactant(newReactant);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
- }
- }
- }
- }
-
- /**
- * Parses xml node for reactanLink and creates reactant from it.
- *
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @param reaction
- * reaction that is being parsed
- * @return reactant obtained from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid and reason is more specific
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", rootNode);
- Species al = (Species) model.getElementByElementId(aliasId);
- if (al == null) {
- throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
- }
-
- Reactant result = new Reactant(al);
- CellDesignerAnchor anchor = null;
- EditPoints points = null;
-
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
- points = parseEditPoints(node);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(), reaction);
- }
- }
- }
-
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
- Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
-
- Point2D endPoint;
-
- Line2D centerLine = reaction.getCenterLine();
-
- double dx = centerLine.getX2() - centerLine.getX1();
- double dy = centerLine.getY2() - centerLine.getY1();
- double coef = REACTANT_END_RATIO;
- endPoint = new Point2D.Double(centerLine.getX1() + dx * coef, centerLine.getY1() + dy * coef);
-
- PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(additionalPoint, endPoint, points);
-
- additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline);
- polyline.setStartPoint(additionalPoint);
- result.setLine(polyline);
-
- return result;
- }
-
- /**
- * Parses xml node with productLink nodes and creates products in the
- * reaction.
- *
- * @param result
- * reaction to be updated
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseProductLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
- NodeList list = rootNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:productLink")) {
- Product link = getProductLink(node, model, result);
- result.addProduct(link);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfProductLinks: " + node.getNodeName(), result);
- }
- }
- }
- }
-
- /**
- * Parses xml node for productLink and creates product from it.
- *
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @param reaction
- * reaction that is being parsed
- * @return product obtained from xml node
- * @throws ReactionParserException
- * thrown when the xml is invalid
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private Product getProductLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", rootNode);
- Species al = (Species) model.getElementByElementId(aliasId);
- if (al == null) {
- throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
- }
-
- Product result = new Product(al);
-
- CellDesignerAnchor anchor = null;
- EditPoints points = null;
-
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
- points = parseEditPoints(node);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(), reaction);
- }
- }
- }
-
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
- Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
- ArrowTypeData atd = new ArrowTypeData();
- atd.setArrowType(ArrowType.NONE);
-
- Point2D endPoint;
-
- // central line points
- Point2D p1 = reaction.getReactants().get(0).getLine().getPoints().get(reaction.getReactants().get(0).getLine().getPoints().size() - 2);
- Point2D p2 = reaction.getProducts().get(0).getLine().getPoints().get(1);
-
- Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
- Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
- for (NodeOperator operator : reaction.getOperators()) {
- toExclude.addAll(operator.getInputs());
- if (operator.isReactantOperator()) {
- toInclude.add(operator);
- // if we have operator in input then central line changes
- p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- }
- if (operator.isProductOperator()) {
- // if we have operator in output then central line changes
- p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
- }
- }
-
- double dx = p2.getX() - p1.getX();
- double dy = p2.getY() - p1.getY();
- double coef = PRODUCT_START_RATIO;
- endPoint = new Point2D.Double(p1.getX() + dx * coef, p1.getY() + dy * coef);
-
- PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(endPoint, additionalPoint, points);
- additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline.reverse());
- polyline.setEndPoint(additionalPoint);
-
- polyline.getEndAtd().setArrowType(ArrowType.FULL);
- result.setLine(polyline);
- return result;
- }
-
- /**
- * Creates {@link LineProperties} object from the node.
- *
- * @param node
- * xml node to parse
- * @return {@link LineProperties} object
- */
- private LineProperties getLineProperties(Node node) {
- LineProperties line = new LineProperties();
- String tmp = getNodeAttr("width", node);
- line.setWidth(Double.parseDouble(tmp));
- tmp = getNodeAttr("color", node);
- line.setColor(stringToColor(tmp));
- line.setType(getNodeAttr("type", node));
- return line;
- }
-
- /**
- * PArse reaction modifiactions and add them into reaction.
- *
- * @param result
- * reaction currently processed
- * @param rootNode
- * xml node to parse
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when the xml is invalid, and reason is more specific
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseReactionModification(Reaction result, Node rootNode, Model model) throws ReactionParserException {
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
- parseModificationReaction(result, node, model);
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(), result);
- }
- }
- }
- }
-
- /**
- * PArses modification node and adds this modification to reaction.
- *
- * @param reaction
- * reaction currently processed
- * @param rootNode
- * xml node
- * @param model
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when node cannot be parsed properly
- */
- private void parseModificationReaction(Reaction reaction, Node rootNode, Model model) throws ReactionParserException {
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- String type = getNodeAttr("type", rootNode);
- String modificationType = getNodeAttr("modificationType", rootNode);
- String aliasId = getNodeAttr("aliases", rootNode);
- String lineConnectionType = getNodeAttr("targetLineIndex", rootNode);
- String points = getNodeAttr("editPoints", rootNode);
-
- List<Species> aliasList = new ArrayList<Species>();
-
- String[] list = aliasId.split(",");
- for (String string : list) {
- Species al = (Species) model.getElementByElementId(string);
- if (al != null) {
- aliasList.add(al);
- } else {
- throw new ReactionParserException("Unknown alias: " + string, reaction);
- }
- }
- Modifier result = null;
- if (aliasList.size() > 1) {
- result = new Modifier(null);
- reaction.addModifier(result);
- for (int i = 0; i < aliasList.size(); i++) {
- Modifier mod = modifierTypeUtils.createModifierForStringType(modificationType, aliasList.get(i));
- modifierParentOperator.put(mod, result);
- reaction.addModifier(mod);
- }
- } else {
- ModifierType mType = modifierTypeUtils.getModifierTypeForStringType(type);
- if (mType == null) {
- String errorInfo = "[" + reaction.getClass().getSimpleName() + "\t" + reaction.getIdReaction() + "]\tUnknown modifier type: " + type;
- if (ReactionLineData.getByCellDesignerString(type) != null) {
- errorInfo += ".\tThis type can be applied to reaction type only, not modifier.";
- }
- throw new UnknownModifierClassException(errorInfo, type, reaction.getIdReaction());
- }
- for (Modifier modifier : reaction.getModifiers()) {
- if (modifier.getElement() == aliasList.get(0) && modifier.getClass() == mType.getClazz()) {
- result = modifier;
- }
- }
- if (result == null) {
- result = modifierTypeUtils.createModifierForStringType(type, aliasList.get(0));
- reaction.addModifier(result);
- }
- }
- pointsByModifier.put(result, parseEditPointsString(points));
- typeByModifier.put(result, type);
- lineTypeByModifier.put(result, lineConnectionType);
-
- NodeList nodes = rootNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
- continue;
- } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkTarget")) {
- try {
- CellDesignerAnchor anchor = getAnchorFromLinkTarget(node);
- anchorsByNodes.put(result, anchor);
- } catch (InvalidXmlSchemaException e) {
- throw new ReactionParserException(reaction, e);
- }
- } else {
- throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(), reaction);
- }
- }
-
- }
-
- }
-
- /**
- * Creates lines for modifiers.
- *
- * @param reaction
- * reaction where modifiers are placed
- * @param modifiers
- * list of modifiers for which lines should be generated
- */
- private void computeLineForModification(Reaction reaction, List<Modifier> modifiers) {
- ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
- Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(reaction, lineTypeByModifier.get(modifiers.get(0)));
-
- Point2D startPoint;
- List<Point2D> subPoints;
- // in case we have more then one alias in modification then we need to
- // define the start point as a different one then one on the alias
- Modifier modifier = modifiers.get(0);
- List<Point2D> points = pointsByModifier.get(modifier);
- startPoint = points.get(points.size() - 1);
- subPoints = points.subList(0, points.size() - 1);
- PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p, subPoints);
- modifier.setLine(line);
-
- Point2D endPoint = startPoint;
-
- for (int i = 1; i < modifiers.size(); i++) {
- Modifier param = modifiers.get(i);
- CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(param.getElement(), sbgn);
- startPoint = reactantConverter.getPointCoordinates(param.getElement(), anchorsByNodes.get(param));
-
- PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint, pointsByModifier.get(param));
-
- startPoint = reactantConverter.getAnchorPointCoordinates(param.getElement(), anchorsByNodes.get(param), polyline);
- polyline.setStartPoint(startPoint);
- param.setLine(polyline);
- }
- }
-
- /**
- * Returns {@link CellDesignerAnchor} point from linkAnchor xml node.
- *
- * @param rootNode
- * xml node
- * @return {@link CellDesignerAnchor} object representing anchor point
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private CellDesignerAnchor getAnchorFromLinkTarget(Node rootNode) throws InvalidXmlSchemaException {
- CellDesignerAnchor result = null;
-
- NodeList nodes = rootNode.getChildNodes();
- for (int z = 0; z < nodes.getLength(); z++) {
- Node node = nodes.item(z);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
- result = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:connectScheme: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Creates {@link ConnectScheme} object from xml node.
- *
- * @param nodeReaction
- * xml node to parse
- * @return {@link ConnectScheme} object for given xml
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private ConnectScheme parseConnectScheme(Node nodeReaction) throws InvalidXmlSchemaException {
- ConnectScheme result = new ConnectScheme();
- result.setConnectPolicy(getNodeAttr("connectPolicy", nodeReaction));
- result.setConnectIndex(getNodeAttr("rectangleIndex", nodeReaction));
- 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:listOfLineDirection")) {
- result.setLineDirections(getlineDirectionMapForReactions(reactantNode));
- } else {
- throw new InvalidXmlSchemaException("Unknown element of celldesigner:connectScheme: " + nodeReaction.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Parse lineDirectionMap. This structure is nowhere used.
- *
- * @param reactantNode
- * xml node
- * @return map with directions for every line
- * @throws InvalidXmlSchemaException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private Map<String, String> getlineDirectionMapForReactions(Node reactantNode) throws InvalidXmlSchemaException {
- Map<String, String> result = new HashMap<String, String>();
- NodeList nodes = reactantNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("celldesigner:lineDirection")) {
- String index = getNodeAttr("index", node);
- String value = getNodeAttr("value", node);
- result.put(index, value);
- } else {
- throw new InvalidXmlSchemaException("Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * 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
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseBaseReactant(Reaction result, Node reactantNode, Model model) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", reactantNode);
- Species alias = (Species) model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
- }
- 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);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- 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);
- }
- }
-
- }
- }
-
- /**
- * 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
- * model where reaction is placed
- * @throws ReactionParserException
- * thrown when xml node contains data that is not supported by xml
- * schema
- */
- private void parseBaseProduct(Model model, Reaction result, Node reactantNode) throws ReactionParserException {
- String aliasId = getNodeAttr("alias", reactantNode);
- Species alias = (Species) model.getElementByElementId(aliasId);
- if (alias == null) {
- throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
- }
- Product product = new Product(alias);
- result.addProduct(product);
- NodeList nodes = reactantNode.getChildNodes();
- for (int x = 0; x < nodes.getLength(); x++) {
- Node node = nodes.item(x);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- 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);
- }
- }
- }
-
- }
+ /**
+ * Reactant lines in cell designer ends in the 2/5 of the center line.
+ */
+ private static final double REACTANT_END_RATIO = 0.4;
+
+ /**
+ * Product lines in cell designer starts in the 3/5 of the center line.
+ */
+ private static final double PRODUCT_START_RATIO = 0.6;
+
+ /**
+ * Stores information about {@link CellDesignerAnchor} for a node.
+ */
+ private Map<ReactionNode, CellDesignerAnchor> anchorsByNodes = new HashMap<ReactionNode, CellDesignerAnchor>();
+
+ /**
+ * Stores information about operator type that should be used for a modifier
+ * node.
+ */
+ private Map<ReactionNode, String> typeByModifier = new HashMap<ReactionNode, String>();
+
+ /**
+ * Stores information to which point on the central rectangle modifier should be
+ * connected.
+ */
+ private Map<ReactionNode, String> lineTypeByModifier = new HashMap<ReactionNode, String>();
+
+ /**
+ * Stores information about list of points that create line describing modifier.
+ */
+ private Map<ReactionNode, List<Point2D>> pointsByModifier = new HashMap<ReactionNode, List<Point2D>>();
+
+ /**
+ * Helps to determine if the key Modifier should be treats as part of
+ * NodeOperator (value in the map).
+ */
+ private Map<Modifier, Modifier> modifierParentOperator = new HashMap<Modifier, Modifier>();
+
+ /**
+ * Identifies central line segment in {@link TwoProductReactionInterface} and
+ * {@link TwoReactantReactionInterface} reactions.
+ */
+ private Map<ReactionNode, Integer> indexByComplexReaction = new HashMap<ReactionNode, Integer>();
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ReactionXmlParser.class.getName());
+
+ /**
+ * Xml parser used for processing notes into structured data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ /**
+ * Helper object used for manipulation on the point coordinates in CellDesigner
+ * format.
+ */
+ private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
+
+ /**
+ * Should SBGN standard be used.
+ */
+ private boolean sbgn;
+
+ /**
+ * Default constructor.
+ *
+ * @param sbgn
+ * Should the converter use SBGN standard
+ */
+ public ReactionFromXml(boolean sbgn) {
+ this.sbgn = sbgn;
+ }
+
+ /**
+ * Returns {@link Reaction} object from CellDesigner xml node.
+ *
+ * @param reactionNode
+ * xml node
+ * @param model
+ * model where the reaction is placed
+ * @return reactin from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when reactionNode is invalid xml
+ */
+ public Reaction getReaction(Node reactionNode, Model model) throws ReactionParserException {
+ Reaction result = new Reaction();
+ // we ignore metaid - it's useless and obstruct data model
+ // result.setMetaId(getNodeAttr("metaid", reactionNode));
+ result.setIdReaction(getNodeAttr("id", reactionNode));
+ result.setName(getNodeAttr("name", reactionNode));
+ // by default this value is true...
+ result.setReversible(!(getNodeAttr("reversible", reactionNode).equalsIgnoreCase("false")));
+
+ NodeList nodes = reactionNode.getChildNodes();
+ Node annotationNode = null;
+ Node kineticsNode = null;
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("annotation")) {
+ annotationNode = node;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfReactants")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfProducts")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("listOfModifiers")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("notes")) {
+ rap.processNotes(rap.getNotes(node), result);
+ } else if (node.getNodeName().equalsIgnoreCase("kineticLaw")) {
+ kineticsNode = node;
+ } else {
+ throw new ReactionParserException("Unknown element of reaction: " + node.getNodeName(), result);
+ }
+ }
+ }
+ if (annotationNode != null) {
+ result = parseReactionAnnotation(annotationNode, result, model);
+ } else {
+ throw new ReactionParserException("No annotation node in reaction", result);
+ }
+ if (kineticsNode != null) {
+ Map<String, Element> elements = getSpeciesIdToElementMappingFromAnnotationNode(annotationNode, model);
+ KineticsXmlParser kineticsParser = new KineticsXmlParser(model);
+ try {
+ result.setKinetics(kineticsParser.parseKinetics(kineticsNode, elements));
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(result, e);
+ }
+ }
+
+ return result;
+ }
+
+ 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) {
+ String speciesId = super.getNodeAttr("species", node);
+ String aliasId = super.getNodeAttr("alias", node);
+ result.put(speciesId, model.getElementByElementId(aliasId));
+ }
+ return result;
+ }
+
+ /**
+ * Parses reaction annotation node and update reaction.
+ *
+ * @param annotationNode
+ * xml node
+ * @param result
+ * reaction to update
+ * @param model
+ * model where reaction is placed
+ * @return updated reaction
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when annotationNode is invalid xml
+ */
+ private Reaction parseReactionAnnotation(Node annotationNode, Reaction result, Model model)
+ throws ReactionParserException {
+ NodeList nodes = annotationNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
+ result = parseReactionExtension(result, node, model);
+ } else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
+ try {
+ XmlAnnotationParser xmlParser = new XmlAnnotationParser();
+ result.addMiriamData(xmlParser.parseRdfNode(nodes));
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException("Problem with parsing RDF", result, e);
+ }
+ } else {
+ throw new ReactionParserException("Unknown element of reaction/annotation: " + node.getNodeName(), result);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Parses CellDesigner extension to sbml reaction node and updates reaction.
+ *
+ * @param result
+ * reaction to update
+ * @param node
+ * xml node
+ * @param model
+ * model where reaction is placed
+ * @return updated reaction
+ * @throws ReactionParserException
+ * thrown when the xml is invalid and reason is more specific
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ *
+ */
+ 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);
+ }
+ }
+ }
+ } 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: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);
+ }
+ }
+ 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);
+
+ // 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);
+ }
+ }
+
+ 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());
+ }
+ }
+
+ return result;
+ }
+
+ /**
+ * Creates reaction with a new type.
+ *
+ * @param type
+ * CellDesigner type of a reaction
+ * @param result
+ * initial data
+ * @return reaction with a new type
+ * @throws UnknownReactionClassException
+ * thrown when type is invalid
+ */
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ ReactionLineData rdl = ReactionLineData.getByCellDesignerString(type);
+ if (rdl == null) {
+ throw new UnknownReactionClassException("Unknown CellDesigner class type: " + type + ".", type,
+ result.getIdReaction());
+ }
+ return rdl.createReaction(result);
+ }
+
+ /**
+ * Creates CellDesigner {@link EditPoints} structure for gate members node.
+ *
+ * @param gateMembers
+ * xml node
+ * @return {@link EditPoints} structure representing line information for the
+ * xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private EditPoints gateMembersToPoints(Node gateMembers) throws InvalidXmlSchemaException {
+ Node lastMember = null;
+ EditPoints result = new EditPoints();
+ Integer num0 = null;
+ Integer num1 = null;
+ Integer num2 = null;
+ for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
+ Node child = gateMembers.getChildNodes().item(i);
+ if (child.getNodeType() == Node.ELEMENT_NODE) {
+
+ if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
+ String type = getNodeAttr("type", child);
+ if (type.startsWith(ReactionLineData.BOOLEAN_LOGIC_GATE.getCellDesignerString())) {
+ lastMember = child;
+ } else {
+ String pointsString = getNodeAttr("editPoints", child);
+ List<Point2D> points = parseEditPointsString(pointsString);
+ if (num0 == null) {
+ num0 = points.size();
+ } else if (num1 == null) {
+ num1 = points.size();
+ } else {
+ throw new InvalidXmlSchemaException("Too many gate members");
+ }
+ result.getPoints().addAll(points);
+ }
+ } else {
+ throw new InvalidXmlSchemaException("Unknown node type: " + child.getNodeName());
+ }
+ }
+ }
+ if (lastMember == null) {
+ throw new InvalidXmlSchemaException("Missing gate member connecting members");
+ } else {
+ String pointsString = getNodeAttr("editPoints", lastMember);
+ List<Point2D> points = parseEditPointsString(pointsString);
+ num2 = points.size() - 1;
+ result.getPoints().addAll(points);
+ }
+ result.setNum0(num0);
+ result.setNum1(num1);
+ result.setNum2(num2);
+ return result;
+ }
+
+ /**
+ * Creates line information for the modifier.
+ *
+ * @param reaction
+ * reaction where modifier is placed
+ * @param modifier
+ * modifier to update
+ */
+ private void createLineForModifier(Reaction reaction, Modifier modifier) {
+ Element element = modifier.getElement();
+ CellDesignerAliasConverter converter = new CellDesignerAliasConverter(element, sbgn);
+ Point2D startPoint = converter.getPointCoordinates(element, anchorsByNodes.get(modifier));
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+
+ Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(),
+ lineTypeByModifier.get(modifier));
+ PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p,
+ pointsByModifier.get(modifier));
+
+ startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
+ line.setStartPoint(startPoint);
+ modifier.setLine(line);
+ modifierTypeUtils.updateLineEndPoint(modifier);
+ }
+
+ /**
+ * Creates operators for CellDesigner reaction that belongs to
+ * {@link TwoProductReactionInterface}.
+ *
+ * @param result
+ * reaction to be updated
+ * @throws ReactionParserException
+ * thrown when there is a problem with creating operators (input data
+ * is invalid)
+ */
+ private void createOperatorsForTwoProductReaction(Reaction result) throws ReactionParserException {
+ int inputs = 0;
+ NodeOperator operator = null;
+ if (result.getClass() == DissociationReaction.class) {
+ operator = new DissociationOperator();
+ } else if (result.getClass() == TruncationReaction.class) {
+ operator = new TruncationOperator();
+ } else {
+ throw new ReactionParserException("Invalid reaction type", result);
+ }
+ for (AbstractNode node : result.getNodes()) {
+ if (node.getClass() == Product.class) {
+ operator.addOutput(node);
+ } else if (node.getClass() == Reactant.class) {
+ inputs++;
+ if (inputs > 1) {
+ throw new ReactionParserException("Reaction has more than one reactant", result);
+ }
+ }
+ }
+ if (operator.getOutputs().size() > 2) {
+ throw new ReactionParserException("Too many products: " + operator.getOutputs().size(), result);
+ }
+
+ // and now we have to modify lines
+
+ Reactant reactant = result.getReactants().get(0);
+ Integer index = indexByComplexReaction.get(reactant);
+
+ Point2D p1, p2;
+
+ p1 = reactant.getLine().getPoints().get(index);
+ p2 = reactant.getLine().getPoints().get(index + 1);
+
+ p1 = new Point2D.Double(p1.getX(), p1.getY());
+ p2 = new Point2D.Double(p2.getX(), p2.getY());
+
+ Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ operator.setLine(reactant.getLine().getSubline(0, index + 1));
+ operator.getLine().addPoint(p);
+
+ p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+
+ reactant.setLine(reactant.getLine().getSubline(index + 1, reactant.getLine().getPoints().size()).reverse());
+ reactant.getLine().getPoints().add(p);
+
+ reactant.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ operator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ result.addNode(operator);
+ }
+
+ /**
+ * Creates general input/output operators for the model.
+ *
+ * @param result
+ * reaction to be updated
+ */
+ private void createOperators(Reaction result) {
+ // central line points
+ Point2D p1 = result.getReactants().get(0).getLine().getPoints()
+ .get(result.getReactants().get(0).getLine().getPoints().size() - 2);
+ Point2D p2 = result.getProducts().get(0).getLine().getPoints().get(1);
+ Point2D tmp = result.getProducts().get(0).getLine().getPoints().get(0);
+ Point2D productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+
+ // where the line from reactants ends
+ tmp = result.getReactants().get(0).getLine().getPoints()
+ .get(result.getReactants().get(0).getLine().getPoints().size() - 1);
+ Point2D reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+
+ Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
+ Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
+ for (NodeOperator operator : result.getOperators()) {
+ toExclude.addAll(operator.getInputs());
+ if (operator.isReactantOperator()) {
+ toInclude.add(operator);
+ // if we have operator in input then central line changes
+ p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
+ reactantAndOperatorEndPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+ }
+ if (operator.isProductOperator()) {
+ // if we have operator in output then central line changes
+ p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ tmp = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 1);
+ productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
+ }
+ }
+
+ double dx = p2.getX() - p1.getX();
+ double dy = p2.getY() - p1.getY();
+
+ Point2D reactantAndOperatorBeginPoint = new Point2D.Double(p1.getX() + dx * REACTANT_END_RATIO,
+ p1.getY() + dy * REACTANT_END_RATIO);
+
+ PolylineData ld = new PolylineData(reactantAndOperatorBeginPoint, reactantAndOperatorEndPoint);
+
+ LineType lineType = null;
+ Set<AbstractNode> nodes = new LinkedHashSet<AbstractNode>();
+ for (Reactant reactant : result.getReactants()) {
+ if (!toExclude.contains(reactant)) {
+ nodes.add(reactant);
+ if (lineType == null) {
+ lineType = reactant.getLine().getType();
+ }
+ }
+ }
+ nodes.addAll(toInclude);
+ nodes.removeAll(toExclude);
+
+ // add an operator only when the number of input nodes is greater than one
+ if (nodes.size() > 1) {
+ AndOperator inputOperator = new AndOperator();
+ inputOperator.setLine(ld);
+ inputOperator.addInputs(nodes);
+ for (Reactant reactant : result.getReactants()) {
+ if (!toExclude.contains(reactant)) {
+ reactant.getLine().getEndPoint().setLocation(reactantAndOperatorBeginPoint.getX(),
+ reactantAndOperatorBeginPoint.getY());
+ }
+ }
+ if (lineType != null) {
+ inputOperator.getLine().setType(lineType);
+ }
+ result.addNode(inputOperator);
+ }
+
+ // and now we try to handle with output operators
+
+ toExclude = new HashSet<AbstractNode>();
+ toInclude = new HashSet<AbstractNode>();
+ for (NodeOperator nOperator : result.getOperators()) {
+ toExclude.addAll(nOperator.getOutputs());
+ if (nOperator.isProductOperator()) {
+ toInclude.add(nOperator);
+ }
+ }
+
+ Point2D productSplitOperatorEndPoint = new Point2D.Double(p1.getX() + dx * PRODUCT_START_RATIO,
+ p1.getY() + dy * PRODUCT_START_RATIO);
+
+ ld = new PolylineData(productSplitOperatorEndPoint, productSplitOperatorBeginPoint);
+
+ lineType = null;
+ nodes = new LinkedHashSet<AbstractNode>();
+ for (Product product : result.getProducts()) {
+ if (!toExclude.contains(product)) {
+ nodes.add(product);
+ if (lineType == null) {
+ lineType = product.getLine().getType();
+ }
+ }
+ }
+ nodes.addAll(toInclude);
+ nodes.removeAll(toExclude);
+ if (nodes.size() > 1) {
+ SplitOperator outputOperator = new SplitOperator();
+ outputOperator.setLine(ld);
+ outputOperator.addOutputs(nodes);
+ for (Product product : result.getProducts()) {
+ if (!toExclude.contains(product)) {
+ // outputOperator.addOutput(product);
+ product.getLine().getPoints().get(0).setLocation(productSplitOperatorEndPoint.getX(),
+ productSplitOperatorEndPoint.getY());
+ }
+ }
+ if (lineType != null) {
+ outputOperator.getLine().setType(lineType);
+ }
+ result.addNode(outputOperator);
+ }
+ }
+
+ /**
+ * Creates operators in modifiers.
+ *
+ * @param reaction
+ * reaction to update
+ * @param modifiers
+ * list of modifiers that must be put into operators
+ */
+ private void createOperatorFromModifiers(Reaction reaction, List<Modifier> modifiers) {
+ OperatorTypeUtils otu = new OperatorTypeUtils();
+ String type = typeByModifier.get(modifiers.get(0));
+ NodeOperator operator = otu.createModifierForStringType(type);
+
+ operator.setLine(modifiers.get(0).getLine());
+
+ for (int i = 1; i < modifiers.size(); i++) {
+ operator.addInput(modifiers.get(i));
+ }
+
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ modifierTypeUtils.updateLineEndPoint(operator);
+ reaction.addNode(operator);
+ }
+
+ /**
+ * Creates operators for CellDesigner reaction that belongs to
+ * {@link TwoReactantReactionInterface}.
+ *
+ * @param result
+ * reaction to be updated
+ * @param gateMembers
+ * node representing line information for the operator
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ */
+ private void createOperatorsForTwoReactantReaction(Reaction result, Node gateMembers) throws ReactionParserException {
+ NodeOperator andOperator = null;
+ if (result instanceof HeterodimerAssociationReaction) {
+ andOperator = new AssociationOperator();
+ } else if (result instanceof BooleanLogicGateReaction) {
+ andOperator = new AndOperator();
+ } else {
+ throw new ReactionParserException("Unknown class type with two reactants", result);
+ }
+ int outputs = 0;
+ for (AbstractNode node : result.getNodes()) {
+ if (node.getClass() == Reactant.class) {
+ andOperator.addInput(node);
+ } else if (node.getClass() == Product.class) {
+ outputs++;
+ if (outputs > 1) {
+ throw new ReactionParserException("Reaction has more than one product", result);
+ }
+ }
+ }
+ if (andOperator.getInputs().size() > 2) {
+ throw new ReactionParserException("Too many reactants.", result);
+ }
+
+ // and now we have to modify lines
+
+ Product product = result.getProducts().get(0);
+ Integer index = indexByComplexReaction.get(product);
+ if (index != null) {
+ Point2D p1, p2;
+
+ p1 = product.getLine().getPoints().get(index);
+ p2 = product.getLine().getPoints().get(index + 1);
+
+ p1 = new Point2D.Double(p1.getX(), p1.getY());
+ p2 = new Point2D.Double(p2.getX(), p2.getY());
+
+ Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ andOperator.setLine(product.getLine().getSubline(0, index + 1));
+ andOperator.getLine().addPoint(p);
+ andOperator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+
+ product.setLine(product.getLine().getSubline(index, product.getLine().getPoints().size()));
+ product.getLine().getPoints().set(0, p);
+ product.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
+
+ result.addNode(andOperator);
+ } else {
+ NodeOperator operator = null;
+ Set<String> undefinedTypes = new HashSet<String>();
+ for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
+ Node child = gateMembers.getChildNodes().item(i);
+ if (child.getNodeType() == Node.ELEMENT_NODE) {
+
+ if (child.getNodeName().equalsIgnoreCase("celldesigner:GateMember")) {
+ String type = getNodeAttr("type", child);
+
+ if (type.equalsIgnoreCase(OperatorType.AND_OPERATOR_STRING.getStringName())) {
+ operator = new AndOperator();
+ } else if (type.equalsIgnoreCase(OperatorType.OR_OPERATOR_STRING.getStringName())) {
+ operator = new OrOperator();
+ } else if (type.equalsIgnoreCase(OperatorType.NAND_OPERATOR_STRING.getStringName())) {
+ operator = new NandOperator();
+ } else if (type.equalsIgnoreCase(OperatorType.UNKNOWN_OPERATOR_STRING.getStringName())) {
+ operator = new UnknownOperator();
+ } else {
+ undefinedTypes.add(type);
+ }
+ }
+ }
+ }
+ if (operator == null) {
+ String types = "";
+ for (String string : undefinedTypes) {
+ types += string + ", ";
+ }
+ throw new ReactionParserException(
+ "Couldn't find type of BOOLEAN_LOGIC_GATE. Unknown types identified: " + types, result);
+ }
+
+ operator.addInputs(andOperator.getInputs());
+ operator.addOutput(product);
+
+ // empty line
+ PolylineData line = new PolylineData();
+ line.addPoint(product.getLine().getBeginPoint());
+ line.addPoint(product.getLine().getBeginPoint());
+
+ operator.setLine(line);
+ result.addNode(operator);
+ }
+
+ }
+
+ /**
+ * Creates lines for reaction that belongs to
+ * {@link TwoProductReactionInterface}.
+ *
+ * @param reaction
+ * reaction to update
+ * @param points
+ * information about points
+ */
+ private void createLinesForTwoProductReaction(Reaction reaction, EditPoints points) {
+ Point2D p = points.getPoints().get(points.size() - 1);
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+ Reactant reactant = reaction.getReactants().get(0);
+
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
+ CellDesignerAliasConverter product1Converter = new CellDesignerAliasConverter(product1.getElement(), sbgn);
+ CellDesignerAliasConverter product2Converter = new CellDesignerAliasConverter(product2.getElement(), sbgn);
+
+ Point2D p1 = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
+ Point2D p2 = product1Converter.getPointCoordinates(product1.getElement(), anchorsByNodes.get(product1));
+ Point2D p3 = product2Converter.getPointCoordinates(product2.getElement(), anchorsByNodes.get(product2));
+
+ Point2D centerPoint = pointTransformation.getCoordinatesInNormalBase(product1.getElement().getCenter(),
+ product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
+
+ int startId0 = 0;
+ int num0 = points.getNum0();
+ int startId1 = num0;
+ int num1 = num0 + points.getNum1();
+ int startId2 = num1;
+ int num2 = num1 + points.getNum2();
+
+ ArrayList<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
+ ArrayList<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
+ ArrayList<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
+
+ PolylineData product1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
+ PolylineData product2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
+
+ PolylineData reactantLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
+
+ p1 = product2Converter.getAnchorPointCoordinates(product2.getElement(), anchorsByNodes.get(product2),
+ product2Line.reverse());
+ product2Line.setEndPoint(p1);
+
+ p1 = product1Converter.getAnchorPointCoordinates(product1.getElement(), anchorsByNodes.get(product1),
+ product1Line.reverse());
+ product1Line.setEndPoint(p1);
+
+ p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant),
+ reactantLine.reverse());
+ reactantLine.setEndPoint(p1);
+
+ product2Line.getEndAtd().setArrowType(ArrowType.FULL);
+ product1Line.getEndAtd().setArrowType(ArrowType.FULL);
+ product1.setLine(product1Line);
+ product2.setLine(product2Line);
+ reactant.setLine(reactantLine);
+
+ indexByComplexReaction.put(reactant, points.getIndex());
+
+ }
+
+ /**
+ * Creates lines for reaction that belongs to
+ * {@link TwoReactantReactionInterface}.
+ *
+ * @param reaction
+ * reaction to update
+ * @param points
+ * information about points
+ * @param hasGateMemebers
+ * does the reaction has gate members
+ * @throws ReactionParserException
+ * thrown when data for reaction is invalid
+ */
+ private void createLinesForTwoReactantReaction(Reaction reaction, EditPoints points, boolean hasGateMemebers)
+ throws ReactionParserException {
+ Point2D p = points.getPoints().get(points.size() - 1);
+ Product product = reaction.getProducts().get(0);
+ Reactant reactant1 = reaction.getReactants().get(0);
+ Reactant reactant2 = reaction.getReactants().get(1);
+ CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
+ CellDesignerAliasConverter reactantConverter1 = new CellDesignerAliasConverter(reactant1.getElement(), sbgn);
+ CellDesignerAliasConverter reactantConverter2 = new CellDesignerAliasConverter(reactant2.getElement(), sbgn);
+ Point2D p1 = reactantConverter1.getPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1));
+ Point2D p2 = reactantConverter2.getPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2));
+ Point2D p3 = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
+
+ Element alias1 = reactant1.getElement();
+ Element alias2 = reactant2.getElement();
+ Element alias3 = product.getElement();
+
+ Point2D pointA = alias2.getCenter();
+ Point2D pointC = alias1.getCenter();
+ Point2D pointB = alias3.getCenter();
+ Point2D pointP = p;
+ Point2D centerPoint = null;
+ if (!hasGateMemebers) {
+ centerPoint = pointTransformation.getCoordinatesInNormalBase(pointA, pointB, pointC, pointP);
+ } else {
+ centerPoint = pointP;
+ }
+
+ int startId0 = 0;
+ int num0 = points.getNum0();
+ int startId1 = num0;
+ int num1 = num0 + points.getNum1();
+ int startId2 = num1;
+ int num2 = num1 + points.getNum2();
+
+ List<Point2D> linePoints1 = new ArrayList<Point2D>(points.getPoints().subList(startId0, num0));
+ List<Point2D> linePoints2 = new ArrayList<Point2D>(points.getPoints().subList(startId1, num1));
+ List<Point2D> linePoints3 = new ArrayList<Point2D>(points.getPoints().subList(startId2, num2));
+
+ PolylineData reactant1Line = null;
+ PolylineData reactant2Line = null;
+ if (!hasGateMemebers) {
+ reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
+ reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p2, linePoints2);
+ } else {
+ reactant1Line = PolylineDataFactory.createPolylineDataFromEditPoints(p1, centerPoint, linePoints1);
+ reactant1Line = reactant1Line.reverse();
+
+ reactant2Line = PolylineDataFactory.createPolylineDataFromEditPoints(p2, centerPoint, linePoints2);
+ reactant2Line = reactant2Line.reverse();
+ }
+
+ PolylineData productLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p3, linePoints3);
+
+ p1 = reactantConverter1.getAnchorPointCoordinates(reactant1.getElement(), anchorsByNodes.get(reactant1),
+ reactant1Line.reverse());
+ reactant1Line.setEndPoint(p1);
+ reactant1Line = reactant1Line.reverse();
+
+ p1 = reactantConverter2.getAnchorPointCoordinates(reactant2.getElement(), anchorsByNodes.get(reactant2),
+ reactant2Line.reverse());
+ reactant2Line.setEndPoint(p1);
+ reactant2Line = reactant2Line.reverse();
+
+ p1 = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
+ productLine.reverse());
+ productLine.setEndPoint(p1);
+ if (hasGateMemebers) {
+ productLine.getEndAtd().setArrowType(ArrowType.OPEN);
+ }
+
+ product.setLine(productLine);
+ reactant1.setLine(reactant1Line);
+ reactant2.setLine(reactant2Line);
+
+ indexByComplexReaction.put(product, points.getIndex());
+ }
+
+ /**
+ * Creates lines for reaction that belongs to {@link SimpleReactionInterface}
+ * (only one standard product and one standard reactant).
+ *
+ * @param reaction
+ * reaction to update
+ * @param editPoints
+ * information about points
+ * @param scheme
+ * some additional information about the line
+ */
+ private void createLinesForSimpleReaction(Reaction reaction, EditPoints editPoints, ConnectScheme scheme) {
+ Product product = reaction.getProducts().get(0);
+ Reactant reactant = reaction.getReactants().get(0);
+ CellDesignerAliasConverter productConverter = new CellDesignerAliasConverter(product.getElement(), sbgn);
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(reactant.getElement(), sbgn);
+
+ Point2D endPoint = productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product));
+ Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
+
+ PolylineData ld = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
+ editPoints.getPoints());
+
+ // first place where the index of rectangle is kept
+ Integer index = editPoints.getIndex();
+
+ // second place where index of rectangle is kept
+ if (index == null) {
+ index = scheme.getConnectIndex();
+ if (index != null) {
+ // but...
+ // direction of the index is reversed...
+ index = ld.getPoints().size() - index - 2;
+ }
+ }
+ // but sometimes there is no information about index...
+ if (index == null) {
+ index = 0;
+ }
+ startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), ld);
+ endPoint = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
+ ld.reverse());
+ ld.getPoints().set(0, startPoint);
+ ld.getPoints().set(ld.getPoints().size() - 1, endPoint);
+
+ PolylineData line = new PolylineData(ld);
+
+ PolylineData reactantLine = line.getSubline(0, ld.getPoints().size() - index - 1);
+ PolylineData productLine = line.getSubline(ld.getPoints().size() - index - 2, ld.getPoints().size());
+
+ Point2D p1 = ld.getPoints().get(ld.getPoints().size() - index - 2);
+ Point2D p2 = ld.getPoints().get(ld.getPoints().size() - index - 1);
+ Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ reactantLine.getPoints().add(p);
+ reactantLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
+ productLine.getPoints().set(0, p);
+ productLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+
+ productLine.getEndAtd().setArrowType(ArrowType.FULL);
+
+ reactant.setLine(reactantLine);
+ product.setLine(productLine);
+
+ ReactionLineData rld = ReactionLineData.getByReactionType(reaction.getClass());
+ reactantLine.setType(rld.getLineType());
+ productLine.setType(rld.getLineType());
+ productLine.getEndAtd().setArrowType(rld.getProductArrowType());
+ productLine.trimEnd(rld.getProductLineTrim());
+ }
+
+ /**
+ * Prepares {@link EditPoints} structure from xml node.
+ *
+ * @param rootNode
+ * xml node
+ * @return {@link EditPoints} object containing CellDesigner line data
+ */
+ private EditPoints parseEditPoints(Node rootNode) {
+ EditPoints result = new EditPoints();
+ String num0 = getNodeAttr("num0", rootNode);
+ String num1 = getNodeAttr("num1", rootNode);
+ String num2 = getNodeAttr("num2", rootNode);
+ if (!num0.equals("")) {
+ result.setNum0(Integer.parseInt(num0));
+ }
+ if (!num1.equals("")) {
+ result.setNum1(Integer.parseInt(num1));
+ }
+ if (!num2.equals("")) {
+ result.setNum2(Integer.parseInt(num2));
+ }
+ String index = getNodeAttr("tShapeIndex", rootNode);
+ if (!index.equals("")) {
+ result.setIndex(Integer.parseInt(index));
+ }
+
+ String pointsString = getNodeValue(rootNode);
+ result.setPoints(parseEditPointsString(pointsString));
+ return result;
+ }
+
+ /**
+ * Parses CellDesigner point by point string.
+ *
+ * @param pointsString
+ * String containing points
+ * @return list of points
+ */
+ ArrayList<Point2D> parseEditPointsString(String pointsString) {
+ ArrayList<Point2D> points2 = new ArrayList<Point2D>();
+ if (pointsString.isEmpty()) {
+ return points2;
+ }
+ String[] points = pointsString.trim().split(" ");
+ for (String string : points) {
+ String[] p = string.split(",");
+ if (p.length != 2) {
+ throw new InvalidArgumentException("Invalid editPoint string: " + string);
+ } else {
+ double posX = Double.parseDouble(p[0]);
+ double posY = Double.parseDouble(p[1]);
+ Point2D point = new Point2D.Double(posX, posY);
+ if (!pointTransformation.isValidPoint(point)) {
+ throw new InvalidArgumentException(
+ "Invalid point parsed from input string: " + string + ". Result point: " + point);
+ }
+ points2.add(point);
+ }
+ }
+ return points2;
+ }
+
+ /**
+ * Parses xml node with reactantLink nodes and creates reactants in the
+ * reaction.
+ *
+ * @param result
+ * reaction to be updated
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseReactantLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
+ NodeList list = rootNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:reactantLink")) {
+ Reactant newReactant = getReactantLink(node, model, result);
+ result.addReactant(newReactant);
+ } else {
+ throw new ReactionParserException(
+ "Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses xml node for reactanLink and creates reactant from it.
+ *
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @param reaction
+ * reaction that is being parsed
+ * @return reactant obtained from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid and reason is more specific
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private Reactant getReactantLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", rootNode);
+ Species al = (Species) model.getElementByElementId(aliasId);
+ if (al == null) {
+ throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
+ }
+
+ Reactant result = new Reactant(al);
+ CellDesignerAnchor anchor = null;
+ EditPoints points = null;
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
+ points = parseEditPoints(node);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
+ reaction);
+ }
+ }
+ }
+
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
+ Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+
+ Point2D endPoint;
+
+ Line2D centerLine = reaction.getCenterLine();
+
+ double dx = centerLine.getX2() - centerLine.getX1();
+ double dy = centerLine.getY2() - centerLine.getY1();
+ double coef = REACTANT_END_RATIO;
+ endPoint = new Point2D.Double(centerLine.getX1() + dx * coef, centerLine.getY1() + dy * coef);
+
+ PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(additionalPoint, endPoint, points);
+
+ additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline);
+ polyline.setStartPoint(additionalPoint);
+ result.setLine(polyline);
+
+ return result;
+ }
+
+ /**
+ * Parses xml node with productLink nodes and creates products in the reaction.
+ *
+ * @param result
+ * reaction to be updated
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseProductLinks(Reaction result, Node rootNode, Model model) throws ReactionParserException {
+ NodeList list = rootNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:productLink")) {
+ Product link = getProductLink(node, model, result);
+ result.addProduct(link);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:listOfProductLinks: " + node.getNodeName(),
+ result);
+ }
+ }
+ }
+ }
+
+ /**
+ * Parses xml node for productLink and creates product from it.
+ *
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @param reaction
+ * reaction that is being parsed
+ * @return product obtained from xml node
+ * @throws ReactionParserException
+ * thrown when the xml is invalid
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private Product getProductLink(Node rootNode, Model model, Reaction reaction) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", rootNode);
+ Species al = (Species) model.getElementByElementId(aliasId);
+ if (al == null) {
+ throw new ReactionParserException("Alias doesn't exist (id: " + aliasId + ")", reaction);
+ }
+
+ Product result = new Product(al);
+
+ CellDesignerAnchor anchor = null;
+ EditPoints points = null;
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ anchor = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:editPoints")) {
+ points = parseEditPoints(node);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
+ reaction);
+ }
+ }
+ }
+
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(al, sbgn);
+ Point2D additionalPoint = reactantConverter.getPointCoordinates(al, anchor);
+ ArrowTypeData atd = new ArrowTypeData();
+ atd.setArrowType(ArrowType.NONE);
+
+ Point2D endPoint;
+
+ // central line points
+ Point2D p1 = reaction.getReactants().get(0).getLine().getPoints()
+ .get(reaction.getReactants().get(0).getLine().getPoints().size() - 2);
+ Point2D p2 = reaction.getProducts().get(0).getLine().getPoints().get(1);
+
+ Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
+ Set<AbstractNode> toInclude = new HashSet<AbstractNode>();
+ for (NodeOperator operator : reaction.getOperators()) {
+ toExclude.addAll(operator.getInputs());
+ if (operator.isReactantOperator()) {
+ toInclude.add(operator);
+ // if we have operator in input then central line changes
+ p1 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ }
+ if (operator.isProductOperator()) {
+ // if we have operator in output then central line changes
+ p2 = operator.getLine().getPoints().get(operator.getLine().getPoints().size() - 2);
+ }
+ }
+
+ double dx = p2.getX() - p1.getX();
+ double dy = p2.getY() - p1.getY();
+ double coef = PRODUCT_START_RATIO;
+ endPoint = new Point2D.Double(p1.getX() + dx * coef, p1.getY() + dy * coef);
+
+ PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(endPoint, additionalPoint, points);
+ additionalPoint = reactantConverter.getAnchorPointCoordinates(al, anchor, polyline.reverse());
+ polyline.setEndPoint(additionalPoint);
+
+ polyline.getEndAtd().setArrowType(ArrowType.FULL);
+ result.setLine(polyline);
+ return result;
+ }
+
+ /**
+ * Creates {@link LineProperties} object from the node.
+ *
+ * @param node
+ * xml node to parse
+ * @return {@link LineProperties} object
+ */
+ private LineProperties getLineProperties(Node node) {
+ LineProperties line = new LineProperties();
+ String tmp = getNodeAttr("width", node);
+ line.setWidth(Double.parseDouble(tmp));
+ tmp = getNodeAttr("color", node);
+ line.setColor(stringToColor(tmp));
+ line.setType(getNodeAttr("type", node));
+ return line;
+ }
+
+ /**
+ * PArse reaction modifiactions and add them into reaction.
+ *
+ * @param result
+ * reaction currently processed
+ * @param rootNode
+ * xml node to parse
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when the xml is invalid, and reason is more specific
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseReactionModification(Reaction result, Node rootNode, Model model) throws ReactionParserException {
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:modification")) {
+ parseModificationReaction(result, node, model);
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
+ result);
+ }
+ }
+ }
+ }
+
+ /**
+ * PArses modification node and adds this modification to reaction.
+ *
+ * @param reaction
+ * reaction currently processed
+ * @param rootNode
+ * xml node
+ * @param model
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when node cannot be parsed properly
+ */
+ private void parseModificationReaction(Reaction reaction, Node rootNode, Model model) throws ReactionParserException {
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ String type = getNodeAttr("type", rootNode);
+ String modificationType = getNodeAttr("modificationType", rootNode);
+ String aliasId = getNodeAttr("aliases", rootNode);
+ String lineConnectionType = getNodeAttr("targetLineIndex", rootNode);
+ String points = getNodeAttr("editPoints", rootNode);
+
+ List<Species> aliasList = new ArrayList<Species>();
+
+ String[] list = aliasId.split(",");
+ for (String string : list) {
+ Species al = (Species) model.getElementByElementId(string);
+ if (al != null) {
+ aliasList.add(al);
+ } else {
+ throw new ReactionParserException("Unknown alias: " + string, reaction);
+ }
+ }
+ Modifier result = null;
+ if (aliasList.size() > 1) {
+ result = new Modifier(null);
+ reaction.addModifier(result);
+ for (int i = 0; i < aliasList.size(); i++) {
+ Modifier mod = modifierTypeUtils.createModifierForStringType(modificationType, aliasList.get(i));
+ modifierParentOperator.put(mod, result);
+ reaction.addModifier(mod);
+ }
+ } else {
+ ModifierType mType = modifierTypeUtils.getModifierTypeForStringType(type);
+ if (mType == null) {
+ String errorInfo = "[" + reaction.getClass().getSimpleName() + "\t" + reaction.getIdReaction()
+ + "]\tUnknown modifier type: " + type;
+ if (ReactionLineData.getByCellDesignerString(type) != null) {
+ errorInfo += ".\tThis type can be applied to reaction type only, not modifier.";
+ }
+ throw new UnknownModifierClassException(errorInfo, type, reaction.getIdReaction());
+ }
+ for (Modifier modifier : reaction.getModifiers()) {
+ if (modifier.getElement() == aliasList.get(0) && modifier.getClass() == mType.getClazz()) {
+ result = modifier;
+ }
+ }
+ if (result == null) {
+ result = modifierTypeUtils.createModifierForStringType(type, aliasList.get(0));
+ reaction.addModifier(result);
+ }
+ }
+ pointsByModifier.put(result, parseEditPointsString(points));
+ typeByModifier.put(result, type);
+ lineTypeByModifier.put(result, lineConnectionType);
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:connectScheme")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:line")) {
+ continue;
+ } else if (node.getNodeName().equalsIgnoreCase("celldesigner:linkTarget")) {
+ try {
+ CellDesignerAnchor anchor = getAnchorFromLinkTarget(node);
+ anchorsByNodes.put(result, anchor);
+ } catch (InvalidXmlSchemaException e) {
+ throw new ReactionParserException(reaction, e);
+ }
+ } else {
+ throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
+ reaction);
+ }
+ }
+
+ }
+
+ }
+
+ /**
+ * Creates lines for modifiers.
+ *
+ * @param reaction
+ * reaction where modifiers are placed
+ * @param modifiers
+ * list of modifiers for which lines should be generated
+ */
+ private void computeLineForModification(Reaction reaction, List<Modifier> modifiers) {
+ ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
+ Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(reaction, lineTypeByModifier.get(modifiers.get(0)));
+
+ Point2D startPoint;
+ List<Point2D> subPoints;
+ // in case we have more then one alias in modification then we need to
+ // define the start point as a different one then one on the alias
+ Modifier modifier = modifiers.get(0);
+ List<Point2D> points = pointsByModifier.get(modifier);
+ startPoint = points.get(points.size() - 1);
+ subPoints = points.subList(0, points.size() - 1);
+ PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p, subPoints);
+ modifier.setLine(line);
+
+ Point2D endPoint = startPoint;
+
+ for (int i = 1; i < modifiers.size(); i++) {
+ Modifier param = modifiers.get(i);
+ CellDesignerAliasConverter reactantConverter = new CellDesignerAliasConverter(param.getElement(), sbgn);
+ startPoint = reactantConverter.getPointCoordinates(param.getElement(), anchorsByNodes.get(param));
+
+ PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
+ pointsByModifier.get(param));
+
+ startPoint = reactantConverter.getAnchorPointCoordinates(param.getElement(), anchorsByNodes.get(param), polyline);
+ polyline.setStartPoint(startPoint);
+ param.setLine(polyline);
+ }
+ }
+
+ /**
+ * Returns {@link CellDesignerAnchor} point from linkAnchor xml node.
+ *
+ * @param rootNode
+ * xml node
+ * @return {@link CellDesignerAnchor} object representing anchor point
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private CellDesignerAnchor getAnchorFromLinkTarget(Node rootNode) throws InvalidXmlSchemaException {
+ CellDesignerAnchor result = null;
+
+ NodeList nodes = rootNode.getChildNodes();
+ for (int z = 0; z < nodes.getLength(); z++) {
+ Node node = nodes.item(z);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:linkAnchor")) {
+ result = CellDesignerAnchor.valueOf(getNodeAttr("position", node).toUpperCase());
+ } else {
+ throw new InvalidXmlSchemaException("Unknown element of celldesigner:connectScheme: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates {@link ConnectScheme} object from xml node.
+ *
+ * @param nodeReaction
+ * xml node to parse
+ * @return {@link ConnectScheme} object for given xml
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private ConnectScheme parseConnectScheme(Node nodeReaction) throws InvalidXmlSchemaException {
+ ConnectScheme result = new ConnectScheme();
+ result.setConnectPolicy(getNodeAttr("connectPolicy", nodeReaction));
+ result.setConnectIndex(getNodeAttr("rectangleIndex", nodeReaction));
+ 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:listOfLineDirection")) {
+ result.setLineDirections(getlineDirectionMapForReactions(reactantNode));
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of celldesigner:connectScheme: " + nodeReaction.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Parse lineDirectionMap. This structure is nowhere used.
+ *
+ * @param reactantNode
+ * xml node
+ * @return map with directions for every line
+ * @throws InvalidXmlSchemaException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private Map<String, String> getlineDirectionMapForReactions(Node reactantNode) throws InvalidXmlSchemaException {
+ Map<String, String> result = new HashMap<String, String>();
+ NodeList nodes = reactantNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("celldesigner:lineDirection")) {
+ String index = getNodeAttr("index", node);
+ String value = getNodeAttr("value", node);
+ result.put(index, value);
+ } else {
+ throw new InvalidXmlSchemaException(
+ "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * 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
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseBaseReactant(Reaction result, Node reactantNode, Model model) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", reactantNode);
+ Species alias = model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
+ }
+ 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);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ 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);
+ }
+ }
+
+ }
+ }
+
+ /**
+ * 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
+ * model where reaction is placed
+ * @throws ReactionParserException
+ * thrown when xml node contains data that is not supported by xml
+ * schema
+ */
+ private void parseBaseProduct(Model model, Reaction result, Node reactantNode) throws ReactionParserException {
+ String aliasId = getNodeAttr("alias", reactantNode);
+ Species alias = (Species) model.getElementByElementId(aliasId);
+ if (alias == null) {
+ throw new ReactionParserException("Alias with id=" + aliasId + " doesn't exist.", result);
+ }
+ Product product = new Product(alias);
+ result.addProduct(product);
+ NodeList nodes = reactantNode.getChildNodes();
+ for (int x = 0; x < nodes.getLength(); x++) {
+ Node node = nodes.item(x);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ 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);
+ }
+ }
+ }
+
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
index aa13beebfc86c0d909c3128cdbb85cebc6978956..5284caf287314aba6947d1f9ee7100cc0f2b44f3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
@@ -5,14 +5,15 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ ReactionCollectionXmlParserTest.class, //
- ReactionFromXmlTest.class, //
- ReactionLineDataTest.class, //
- ReactionParserExceptionTest.class, //
- ReactionParserTests.class, //
- ReactionToXmlTest.class, //
- UnknownModifierClassExceptionTest.class, //
- UnknownReactionClassExceptionTest.class,//
+@SuiteClasses({ KineticsXmlParserTest.class, //
+ ReactionCollectionXmlParserTest.class, //
+ ReactionFromXmlTest.class, //
+ ReactionLineDataTest.class, //
+ ReactionParserExceptionTest.class, //
+ ReactionParserTests.class, //
+ ReactionToXmlTest.class, //
+ UnknownModifierClassExceptionTest.class, //
+ UnknownReactionClassExceptionTest.class,//
})
public class AllReactionTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..e8e388baec1591aa21b17827f28411e507dabc20
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/KineticsXmlParserTest.java
@@ -0,0 +1,116 @@
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.junit.Test;
+import org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class KineticsXmlParserTest extends CellDesignerTestFunctions {
+
+ @Test
+ public void testParserElements() throws InvalidXmlSchemaException, IOException {
+ Map<String, Element> elements = getTestElementMap();
+ Model model = new ModelFullIndexed(null);
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/simple.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+ assertNotNull(kinetics);
+ assertEquals(2, kinetics.getArguments().size());
+ }
+
+ @Test
+ public void testParserParameters() throws InvalidXmlSchemaException, IOException {
+ Map<String, Element> elements = getTestElementMap();
+ Model model = new ModelFullIndexed(null);
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_parameter.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+ assertNotNull(kinetics);
+ assertEquals(1, kinetics.getParameters().size());
+ }
+
+ @Test
+ public void testParserWithUsedParameters() throws InvalidXmlSchemaException, IOException {
+ Map<String, Element> elements = getTestElementMap();
+ Model model = new ModelFullIndexed(null);
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_used_parameter.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+ assertNotNull(kinetics);
+ assertEquals(1, kinetics.getParameters().size());
+ }
+
+ @Test
+ public void testParserGlobalParameters() throws InvalidXmlSchemaException, IOException {
+ Map<String, Element> elements = getTestElementMap();
+ Model model = new ModelFullIndexed(null);
+ model.addParameter(new SbmlParameter("k1"));
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_global_parameter.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+ assertNotNull(kinetics);
+ assertEquals(1, kinetics.getParameters().size());
+ }
+
+ @Test
+ public void testParserGlobalFunction() throws InvalidXmlSchemaException, IOException {
+ Map<String, Element> elements = getTestElementMap();
+ Model model = new ModelFullIndexed(null);
+ model.addFunction(new SbmlFunction("fun"));
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/with_function.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+ assertNotNull(kinetics);
+ assertEquals(1, kinetics.getFunctions().size());
+ }
+
+ @Test(expected = InvalidXmlSchemaException.class)
+ public void testParserNonExistingElements() throws InvalidXmlSchemaException, IOException {
+ Map<String, Element> elements = new HashMap<>();
+ Model model = new ModelFullIndexed(null);
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/simple.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ parser.parseKinetics(node, elements);
+ }
+
+ @Test
+ public void testParserElementDuplicate() throws InvalidXmlSchemaException, IOException {
+ Model model = new ModelFullIndexed(null);
+ Map<String, Element> elements = getTestElementMap();
+ Node node = super.getXmlDocumentFromFile("testFiles/kinetics/math_using_one_element.xml").getFirstChild();
+
+ KineticsXmlParser parser = new KineticsXmlParser(model);
+ SbmlKinetics kinetics = parser.parseKinetics(node, elements);
+ assertNotNull(kinetics);
+ assertEquals(1, kinetics.getArguments().size());
+ }
+
+ private Map<String, Element> getTestElementMap() {
+ Map<String, Element> elements = new HashMap<>();
+ elements.put("s1", new GenericProtein("s1"));
+ elements.put("s2", new GenericProtein("s2"));
+ return elements;
+ }
+
+}
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 1f6ca70dce3f996bd9473bf623cf958920c30ddc..6b027c8e0fb97aabc608dd348bba37106e704cac 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
@@ -23,637 +23,645 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
public class ReactionFromXmlTest extends CellDesignerTestFunctions {
- ReactionXmlParser parser;
- Model model = new ModelFullIndexed(null);
-
- CellDesignerElementCollection elements;
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
- parser = new ReactionXmlParser(elements, false);
-
- Species alias = new GenericProtein("sa1");
- model.addElement(alias);
-
- alias = new GenericProtein("sa2");
- model.addElement(alias);
-
- alias = new GenericProtein("sa3");
- model.addElement(alias);
-
- alias = new GenericProtein("sa4");
- model.addElement(alias);
-
- elements.addElement(new CellDesignerGenericProtein("s1"));
- elements.addElement(new CellDesignerGenericProtein("s2"));
- elements.addElement(new CellDesignerGenericProtein("s3"));
- elements.addElement(new CellDesignerGenericProtein("s4"));
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testInvalid() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("kineticLaw node doesn't have math subnode"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid2() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction2.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("invalid value in math xmlns attrib"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid3() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction3.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid4() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction4.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("No annotation node in reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid5() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction5.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Problem with parsing RDF"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid6() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction6.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of reaction/annotation"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid7() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction7.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseReactants"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid8() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction8.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseProducts"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid9() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction9.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid10() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction10.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown element of reaction/celldesigner:extension"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid11() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction11.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("No connectScheme node"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid12() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction12.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown node type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid13() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction13.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Too many gate members"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid14() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction14.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Missing gate member connecting members"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid15() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction15.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Couldn't find type of BOOLEAN_LOGIC_GATE"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid16() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction16.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:listOfReactantLinks"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid17() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction17.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid19() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction19.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid20() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction20.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:listOfProductLinks"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid21() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction21.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid23() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction23.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid24() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction24.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid26() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction26.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown alias"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid28() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction28.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid29() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction29.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid30() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction30.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid31() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction31.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid33() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction33.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid34() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction34.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalid36() throws Exception {
- try {
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction36.xml")), model);
- fail("Exception expected");
- } catch (ReactionParserException e) {
- assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown element of reaction/celldesigner:baseProduct"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction() throws Exception {
- try {
- // test situation when createProperTypeReaction returns reaction of
- // unknown type
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- return result;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Problem with parsing lines. Unknown reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction2() throws Exception {
- try {
- // test situation when createProperTypeReaction returns reaction of
- // unknown type that implements TwoProductReactionInterface
-
- class NewReactionType extends Reaction implements TwoProductReactionInterface {
- private static final long serialVersionUID = 1L;
-
- public NewReactionType(Reaction r) {
- super(r);
- }
- }
-
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- return new NewReactionType(result);
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Invalid reaction type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction3() throws Exception {
- try {
- // test situation when createOperatorsForTwoProductReaction encounter
- // reaction with two many base reactants
-
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addReactant(new Reactant());
- return r;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Reaction has more than one reactant"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction4() throws Exception {
- try {
- // test situation when createOperatorsForTwoProductReaction encounter
- // reaction with two many base products
-
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addProduct(new Product());
- return r;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Too many products"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction5() throws Exception {
- try {
- // test situation when createProperTypeReaction returns reaction of
- // unknown type that implements TwoReactantReactionInterface
-
- class NewReactionType extends Reaction implements TwoReactantReactionInterface {
- private static final long serialVersionUID = 1L;
-
- public NewReactionType(Reaction r) {
- super(r);
- }
- }
-
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- return new NewReactionType(result);
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Unknown class type with two reactants"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction6() throws Exception {
- try {
- // test situation when createOperatorsForTwoReactantReaction encounter
- // reaction with two many base reactants
-
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addReactant(new Reactant());
- return r;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Too many reactants"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testInvalidReaction7() throws Exception {
- try {
- // test situation when createOperatorsForTwoReactantReaction encounter
- // reaction with two many base products
-
- ReactionFromXml parser = new ReactionFromXml(false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
- Reaction r = super.createProperTypeReaction(type, result);
- r.addProduct(new Product());
- return r;
- }
- };
- parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")), model);
- fail("Exception expected");
-
- } catch (ReactionParserException e) {
- assertTrue(e.getMessage().contains("Reaction has more than one product"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidEditPointsString() throws Exception {
- try {
- ReactionFromXml parser = new ReactionFromXml(false);
-
- parser.parseEditPointsString("1");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid editPoint string"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testParseInvalidEditPointsString2() throws Exception {
- try {
- ReactionFromXml parser = new ReactionFromXml(false);
-
- parser.parseEditPointsString("1,Infinity");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Invalid point parsed from input string"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ ReactionXmlParser parser;
+ Model model = new ModelFullIndexed(null);
+
+ CellDesignerElementCollection elements;
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+ parser = new ReactionXmlParser(elements, false);
+
+ Species alias = new GenericProtein("sa1");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa2");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa3");
+ model.addElement(alias);
+
+ alias = new GenericProtein("sa4");
+ model.addElement(alias);
+
+ elements.addElement(new CellDesignerGenericProtein("s1"));
+ elements.addElement(new CellDesignerGenericProtein("s2"));
+ elements.addElement(new CellDesignerGenericProtein("s3"));
+ elements.addElement(new CellDesignerGenericProtein("s4"));
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testInvalid() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("kineticLaw node doesn't have math subnode"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid3() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction3.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid4() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction4.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("No annotation node in reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid5() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction5.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Problem with parsing RDF"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid6() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction6.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of reaction/annotation"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid7() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction7.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseReactants"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid8() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction8.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of celldesigner:baseProducts"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid9() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction9.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid10() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction10.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown element of reaction/celldesigner:extension"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid11() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction11.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("No connectScheme node"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid12() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction12.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown node type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid13() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction13.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Too many gate members"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid14() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction14.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Missing gate member connecting members"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid15() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction15.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Couldn't find type of BOOLEAN_LOGIC_GATE"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid16() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction16.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfReactantLinks"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid17() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction17.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid19() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction19.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid20() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction20.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfProductLinks"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid21() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction21.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:reactantLink"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid23() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction23.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias doesn't exist"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid24() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction24.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid26() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction26.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Unknown alias"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid28() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction28.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:connectScheme"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid29() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction29.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of celldesigner:listOfModification"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid30() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction30.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid31() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction31.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid33() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction33.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of reaction/celldesigner:baseReactant"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid34() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction34.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(), e.getMessage().contains("Alias with id"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalid36() throws Exception {
+ try {
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/invalid/reaction36.xml")), model);
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue("Invalid message: " + e.getMessage(),
+ e.getMessage().contains("Unknown element of reaction/celldesigner:baseProduct"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction() throws Exception {
+ try {
+ // test situation when createProperTypeReaction returns reaction of
+ // unknown type
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ return result;
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Problem with parsing lines. Unknown reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction2() throws Exception {
+ try {
+ // test situation when createProperTypeReaction returns reaction of
+ // unknown type that implements TwoProductReactionInterface
+
+ class NewReactionType extends Reaction implements TwoProductReactionInterface {
+ private static final long serialVersionUID = 1L;
+
+ public NewReactionType(Reaction r) {
+ super(r);
+ }
+ }
+
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ return new NewReactionType(result);
+ }
+ };
+ parser.getReaction(
+ super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Invalid reaction type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction3() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoProductReaction encounter
+ // reaction with two many base reactants
+
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addReactant(new Reactant());
+ return r;
+ }
+ };
+ parser.getReaction(
+ super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Reaction has more than one reactant"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction4() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoProductReaction encounter
+ // reaction with two many base products
+
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addProduct(new Product());
+ return r;
+ }
+ };
+ parser.getReaction(
+ super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Too many products"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction5() throws Exception {
+ try {
+ // test situation when createProperTypeReaction returns reaction of
+ // unknown type that implements TwoReactantReactionInterface
+
+ class NewReactionType extends Reaction implements TwoReactantReactionInterface {
+ private static final long serialVersionUID = 1L;
+
+ public NewReactionType(Reaction r) {
+ super(r);
+ }
+ }
+
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ return new NewReactionType(result);
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Unknown class type with two reactants"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction6() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoReactantReaction encounter
+ // reaction with two many base reactants
+
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addReactant(new Reactant());
+ return r;
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Too many reactants"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInvalidReaction7() throws Exception {
+ try {
+ // test situation when createOperatorsForTwoReactantReaction encounter
+ // reaction with two many base products
+
+ ReactionFromXml parser = new ReactionFromXml(false) {
+ Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction r = super.createProperTypeReaction(type, result);
+ r.addProduct(new Product());
+ return r;
+ }
+ };
+ parser.getReaction(super.getNodeFromXmlString(readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml")),
+ model);
+ fail("Exception expected");
+
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Reaction has more than one product"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidEditPointsString() throws Exception {
+ try {
+ ReactionFromXml parser = new ReactionFromXml(false);
+
+ parser.parseEditPointsString("1");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid editPoint string"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testParseInvalidEditPointsString2() throws Exception {
+ try {
+ ReactionFromXml parser = new ReactionFromXml(false);
+
+ parser.parseEditPointsString("1,Infinity");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Invalid point parsed from input string"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
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 021defcdef353c794fe9846034df35ca797d097c..f9f7d558536e5d673a6e6568aee71cdd940a1563 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
@@ -59,1739 +59,1801 @@ import lcsb.mapviewer.model.map.species.Species;
public class ReactionParserTests extends CellDesignerTestFunctions {
- private Logger logger = Logger.getLogger(ReactionParserTests.class.getName());;
- ReactionXmlParser parser;
- CellDesignerElementCollection elements;
-
- @Before
- public void setUp() throws Exception {
- elements = new CellDesignerElementCollection();
-
- parser = new ReactionXmlParser(elements, false);
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testColorReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/colorfull_reaction.xml");
- Reaction reaction = model.getReactionByReactionId("re1");
- PolylineData line = reaction.getReactants().get(0).getLine();
- assertFalse("000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
- line = reaction.getProducts().get(0).getLine();
- assertFalse("000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
- line = reaction.getModifiers().get(0).getLine();
- assertFalse("000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
- line = reaction.getOperators().get(0).getLine();
- assertFalse("000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testMissingLines() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/pd_map_with_problematic_reaction_line.xml");
- assertTrue(model.getElementByElementId("sa5003") instanceof GenericProtein);
- Set<Reaction> list = model.getReactions();
- for (Reaction reaction : list) {
- // reaction re1607 in this model was problematic, but in fact the
- // problem
- // can be in any reaction line
- // if (reaction.getId().equals("re1607")) {
- List<Line2D> lines = reaction.getLines();
- for (Line2D line2d : lines) {
- assertFalse(Double.isNaN(line2d.getX1()));
- assertFalse(Double.isNaN(line2d.getX2()));
- assertFalse(Double.isNaN(line2d.getY1()));
- assertFalse(Double.isNaN(line2d.getY2()));
- }
- // }
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransitionReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transition.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof StateTransitionReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
-
- assertTrue(reaction.isReversible());
- assertEquals(ArrowType.FULL, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(3, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(2, product.getLine().getLines().size());
-
- assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCenterLineInSimpleReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transition.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- Reactant reactant = reaction.getReactants().get(0);
-
- Product product = reaction.getProducts().get(0);
-
- // center of the line should be different than edge points of
- // reactant/product description
- assertFalse(reaction.getCenterLine().getP1().distance(reactant.getLine().getEndPoint()) < 1e-6);
- assertFalse(reaction.getCenterLine().getP2().distance(product.getLine().getBeginPoint()) < 1e-6);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransition2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transitionWithAdditionalNodes.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(2, reaction.getOperators().size());
- for (Reactant reactant : reaction.getReactants()) {
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
-
- assertTrue(reactant.getLine().getEndPoint().distance(reaction.getReactants().get(0).getLine().getEndPoint()) < 1e-6);
- }
-
- for (Product product : reaction.getProducts()) {
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
-
- assertTrue(product.getLine().getBeginPoint().distance(reaction.getProducts().get(0).getLine().getBeginPoint()) < 1e-6);
- }
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransiotionOmitted() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transition_omitted.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(0, reaction.getOperators().size());
- assertEquals(KnownTransitionOmittedReaction.class, reaction.getClass());
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUnknownTransition() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/unknown_transition.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTranscription() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transcription.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TranscriptionReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
- assertEquals(1, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
- assertNotNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTranscription2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transcription_with_additions.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TranscriptionReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
- assertEquals(1, reactant.getLine().getLines().size());
- NodeOperator operator = null;
- for (NodeOperator operator2 : reaction.getOperators()) {
- if (operator2 instanceof SplitOperator)
- operator = operator2;
- }
- assertEquals(LineType.DASH_DOT_DOT, operator.getLine().getType());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTranslation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/translation.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TranslationReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(LineType.DASH_DOT, reactant.getLine().getType());
- assertEquals(1, reactant.getLine().getLines().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.DASH_DOT, operator.getLine().getType());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransport() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/transport.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TransportReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(1, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL_CROSSBAR, product.getLine().getEndAtd().getArrowType());
- assertEquals(1, product.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHeterodimer() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/heterodimer.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof HeterodimerAssociationReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
- reactant = reaction.getReactants().get(1);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(3, reactant.getLine().getLines().size());
-
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(3, product.getLine().getLines().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(7, operator.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testHeterodimerWithAdditions() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/heterodimerWithAdditions.xml");
-
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof HeterodimerAssociationReaction);
- assertEquals(3, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
- reactant = reaction.getReactants().get(1);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(3, reactant.getLine().getLines().size());
-
- for (Product product : reaction.getProducts()) {
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- }
-
- assertEquals(3, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(7, operator.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDissociation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/dissociation.xml");
- assertEquals(2, model.getReactions().size());
- Reaction reaction = null;
- for (Reaction reaction2 : model.getReactions()) {
- if (reaction2.getIdReaction().equals("re1"))
- reaction = reaction2;
- }
- assertTrue(reaction instanceof DissociationReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
-
- assertEquals(2, reaction.getProducts().size());
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(5, product.getLine().getLines().size());
- product = reaction.getProducts().get(1);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(4, product.getLine().getLines().size());
-
- assertEquals(1, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(5, operator.getLine().getLines().size());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testDissociationWithAddition() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/dissociationWithAddition.xml");
- assertEquals(2, model.getReactions().size());
- Reaction reaction = null;
- for (Reaction reaction2 : model.getReactions()) {
- if (reaction2.getIdReaction().equals("re1"))
- reaction = reaction2;
- }
- assertTrue(reaction instanceof DissociationReaction);
- assertEquals(2, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
-
- assertEquals(3, reaction.getProducts().size());
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(5, product.getLine().getLines().size());
- product = reaction.getProducts().get(1);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(4, product.getLine().getLines().size());
-
- assertEquals(3, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(5, operator.getLine().getLines().size());
- assertEquals(DissociationOperator.class, operator.getClass());
-
- assertNotNull(reaction.getReactionRect());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTruncation() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/truncation.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof TruncationReaction);
- assertEquals(1, reaction.getReactants().size());
- Reactant reactant = reaction.getReactants().get(0);
- assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
- assertEquals(2, reactant.getLine().getLines().size());
-
- assertEquals(2, reaction.getProducts().size());
- Product product = reaction.getProducts().get(0);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(3, product.getLine().getLines().size());
- product = reaction.getProducts().get(1);
- assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
- assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
- assertEquals(4, product.getLine().getLines().size());
-
- assertEquals(1, reaction.getOperators().size());
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(LineType.SOLID, operator.getLine().getType());
- assertEquals(1, operator.getLine().getLines().size());
- assertEquals(TruncationOperator.class, operator.getClass());
- assertEquals(reaction.getReactionRect(), ReactionRect.RECT_BOLT);
-
- assertNotNull(reaction.getReactionRect());
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTruncationWithModifier() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/truncationWithModifier.xml");
- Reaction reaction = model.getReactions().iterator().next();
- Modifier m = reaction.getModifiers().get(0);
- assertEquals(ArrowType.CIRCLE, m.getLine().getEndAtd().getArrowType());
-
- m = reaction.getModifiers().get(1);
- assertEquals(ArrowType.CROSSBAR, m.getLine().getEndAtd().getArrowType());
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier1() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier1.xml");
-
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(AndOperator.class, operator.getClass());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier2.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(OrOperator.class, operator.getClass());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier3() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier3.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(NandOperator.class, operator.getClass());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifier4() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier4.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getModifiers().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertTrue(operator.isModifierOperator());
- assertEquals(UnknownOperator.class, operator.getClass());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexReaction.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(0, reaction.getModifiers().size());
- assertEquals(2, reaction.getOperators().size());
- assertEquals(2, reaction.getProducts().size());
- assertEquals(2, reaction.getReactants().size());
-
- NodeOperator operator = reaction.getOperators().iterator().next();
- assertEquals(AndOperator.class, operator.getClass());
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0,false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testComplexModifiers5() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexModifier5.xml");
-
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(4, reaction.getModifiers().size());
- assertEquals(1, reaction.getOperators().size());
- assertEquals(2, reaction.getOperators().iterator().next().getInputs().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchors() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/problemWithAnchors2.xml");
-
- Reaction reaction1 = null;
- Reaction reaction2 = null;
- for (Reaction reaction : model.getReactions()) {
- if (reaction.getIdReaction().equals("re2"))
- reaction1 = reaction;
- if (reaction.getIdReaction().equals("re3"))
- reaction2 = reaction;
- }
- Reactant reactant = reaction1.getReactants().get(0);
- Element alias1 = reaction1.getReactants().get(0).getElement();
- Element alias2 = reaction1.getProducts().get(0).getElement();
- Product product = reaction1.getProducts().get(0);
- Point2D point = new Point2D.Double(alias1.getX() + alias1.getWidth() / 2, alias1.getY() + alias1.getHeight());
- Point2D point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
- assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
- assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
-
- reactant = reaction2.getReactants().get(0);
- alias1 = reaction2.getReactants().get(0).getElement();
- alias2 = reaction2.getProducts().get(0).getElement();
- product = reaction2.getProducts().get(0);
- point = new Point2D.Double(alias1.getX() + alias1.getWidth(), alias1.getY() + alias1.getHeight() / 2);
- point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
- assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
- assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchors3() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/problemWithAnchors3.xml");
- Reaction reaction = null;
- for (Reaction reaction2 : model.getReactions()) {
- if (reaction2.getIdReaction().equals("re3"))
- reaction = reaction2;
- }
- Point2D point = new Point2D.Double(164.85583789974368, 86.060142902597);
- Point2D point2 = new Point2D.Double(397.06477630152193, 284.99999999999994);
-
- assertTrue(point.distance(reaction.getModifiers().get(0).getLine().getPoints().get(0)) < 1);
- assertTrue(point2.distance(reaction.getModifiers().get(1).getLine().getPoints().get(0)) < 1);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testPositiveInfluence() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/positive_influence.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertNull(reaction.getReactionRect());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchors2() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/complexReactionWithModifier.xml");
- Reaction reaction = model.getReactions().iterator().next();
- assertEquals(reaction.getProducts().get(0).getLine().length(), reaction.getReactants().get(0).getLine().length(), 1e-6);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicAnchorsWithTwoReactantReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
- Reaction reaction = model.getReactions().iterator().next();
- Reactant r = null;
- for (Reactant reactant : reaction.getReactants()) {
- if (reactant.getElement().getName().equals("s3")) {
- r = reactant;
- }
- }
- assertNotNull(r);
- // I think there is still a bug becaue it should work with smaller delta
- // :)
- assertEquals(r.getLine().getPoints().get(1).getX(), r.getLine().getPoints().get(2).getX(), 1);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionWithModifiers() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithModifiers.xml");
- Reaction reaction = model.getReactions().iterator().next();
- List<Modifier> modifiers = reaction.getModifiers();
- Modifier sa3 = null;
- Modifier sa4 = null;
- for (Modifier modifier : modifiers) {
- if (modifier.getElement().getElementId().equals("sa3")) {
- sa3 = modifier;
- }
- if (modifier.getElement().getElementId().equals("sa4")) {
- sa4 = modifier;
- }
- }
- assertEquals(sa3.getLine().getPoints().get(0).distance(new Point2D.Double(101.9591678008944, 68.0)), 0, EPSILON);
- assertEquals(sa3.getLine().getPoints().get(1).distance(new Point2D.Double(101.86750788643532, 112.89589905362774)), 0, EPSILON);
- assertEquals(sa3.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0, EPSILON);
-
- assertEquals(sa4.getLine().getPoints().get(0).distance(new Point2D.Double(267.7075561388218, 54.00000000000001)), 0, EPSILON);
- assertEquals(sa4.getLine().getPoints().get(1).distance(new Point2D.Double(298.3735877669656, 71.67109819284718)), 0, EPSILON);
- assertEquals(sa4.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0, EPSILON);
-
- // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
- // false).saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionOperatorsWithOperators() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
- Reaction reaction = model.getReactions().iterator().next();
- NodeOperator operator1 = reaction.getOperators().get(0);
- NodeOperator operator2 = reaction.getOperators().get(1);
- NodeOperator operator3 = reaction.getOperators().get(2);
-
- // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
- // false).saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- assertEquals(operator1.getLine().getPoints().get(0).distance(new Point2D.Double(287.0, 242.00000000000009)), 0, EPSILON);
- assertEquals(operator1.getLine().getPoints().get(1).distance(new Point2D.Double(287.97349260719136, 204.40292958328325)), 0, EPSILON);
- assertEquals(operator1.getLine().getPoints().get(2).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0, EPSILON);
-
- assertEquals(operator2.getLine().getPoints().get(0).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0, EPSILON);
- assertEquals(operator2.getLine().getPoints().get(1).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0, EPSILON);
-
- assertEquals(operator3.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0, EPSILON);
- assertEquals(operator3.getLine().getPoints().get(1).distance(new Point2D.Double(380.9866634960982, 203.80442011470782)), 0, EPSILON);
-
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
-
- assertEquals(product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0, EPSILON);
- assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0, EPSILON);
-
- assertEquals(product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0, EPSILON);
- assertEquals(product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0, EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionProductsWithOperators() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
- Reaction reaction = model.getReactions().iterator().next();
-
- Product product1 = reaction.getProducts().get(0);
- Product product2 = reaction.getProducts().get(1);
-
- assertEquals(product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0, EPSILON);
- assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0, EPSILON);
-
- assertEquals(product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0, EPSILON);
- assertEquals(product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0, EPSILON);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionReactantsWithOperators() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
- Reaction reaction = model.getReactions().iterator().next();
-
- Reactant reactant1 = reaction.getReactants().get(0);
- Reactant reactant2 = reaction.getReactants().get(1);
- Reactant reactant3 = reaction.getReactants().get(2);
-
- assertEquals(reactant1.getLine().getPoints().get(0).distance(new Point2D.Double(112.53618421052632, 167.46381578947367)), 0, EPSILON);
- assertEquals(reactant1.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0, EPSILON);
-
- assertEquals(reactant2.getLine().getPoints().get(0).distance(new Point2D.Double(121.0, 242.0)), 0, EPSILON);
- assertEquals(reactant2.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0, EPSILON);
-
- assertEquals(reactant3.getLine().getPoints().get(0).distance(new Point2D.Double(116.65392247520951, 72.34607752479052)), 0, EPSILON);
- assertEquals(reactant3.getLine().getPoints().get(1).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0, EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testTransitionReactionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition.xml");
-
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
- Reactant reactant1 = reaction1.getReactants().get(0);
- Reactant reactant2 = reaction2.getReactants().get(0);
- assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
- assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
- assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
-
- Product product1 = reaction1.getProducts().get(0);
- Product product2 = reaction2.getProducts().get(0);
- assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
- assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
- assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
-
- assertEquals(reactant1.getLine().getEndPoint().getX(), reactant2.getLine().getEndPoint().getX(), EPSILON);
- assertEquals(reactant1.getLine().getEndPoint().getY(), reactant2.getLine().getEndPoint().getY(), EPSILON);
-
- assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
- assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTransitionWidthAdditionalNodelReactionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
- Reactant reactant1 = reaction1.getReactants().get(1);
- Reactant reactant2 = reaction2.getReactants().get(1);
- assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
- assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
- assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
-
- Product product1 = reaction1.getProducts().get(1);
- Product product2 = reaction2.getProducts().get(1);
- assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
- assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
- assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
-
- assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
- assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
- assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTranslationToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_translation.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
- Reactant reactant1 = reaction1.getReactants().get(1);
- Reactant reactant2 = reaction2.getReactants().get(1);
- assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
- assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
- assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
-
- Product product1 = reaction1.getProducts().get(1);
- Product product2 = reaction2.getProducts().get(1);
- assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
- assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
- assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
-
- assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
- assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
- assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
-
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTransportToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- assertEquals(reaction1.getMiriamData().size(), reaction2.getMiriamData().size());
- assertEquals(reaction1.getNotes().trim(), reaction2.getNotes().trim());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTruncationToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncation.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTruncationWithModifierToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
-
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testUnknownTransitionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTransitionOmittedToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTranscriptionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testTranscriptionWithAdditionsToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionWithOperatorsToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_operators.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionWithModifiersToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
-
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionPositiveInfluenceToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_positive_influence.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionHeterodimerWithAdditionsToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionHeterodimerToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
-
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testOperatorInReactionHeterodimer() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
- for (NodeOperator operator : reaction1.getOperators()) {
- assertTrue(operator instanceof AssociationOperator);
- }
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- @Test
- public void testReactionDissociationWithAdditionToXml() throws Exception {
- try {
- Model model = getModelFilledWithSpecies();
- String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml");
- Node node = getNodeFromXmlString(xmlString);
- Reaction reaction1 = parser.getReaction(node, model);
-
- String xmlString2 = parser.toXml(reaction1);
- assertNotNull(xmlString2);
- // logger.debug(xmlString2);
- Node node2 = getNodeFromXmlString(xmlString2);
- Reaction reaction2 = parser.getReaction(node2, model);
-
- assertEquals(reaction1.getName(), reaction2.getName());
- assertNotNull(reaction1.getName());
- assertFalse(reaction1.getName().trim().equals(""));
- List<Line2D> lines1 = reaction1.getLines();
- List<Line2D> lines2 = reaction2.getLines();
-
- for (int i = 0; i < lines1.size(); i++) {
- assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
- assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
- assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
- assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
- }
- assertEquals(reaction1.getClass(), reaction2.getClass());
- } catch (Exception e) {
- logger.error(e.getMessage(), e);
- throw e;
- }
- }
-
- private Model getModelFilledWithSpecies() {
- Model model = new ModelFullIndexed(null);
-
- Species sa1 = new GenericProtein("sa1");
- sa1.setX(100.0);
- sa1.setY(200.0);
- sa1.setWidth(300.0);
- sa1.setHeight(400.0);
- model.addElement(sa1);
- elements.addModelElement(sa1, new CellDesignerGenericProtein("s1"));
-
- Species sa2 = new GenericProtein("sa2");
- sa2.setX(1050.0);
- sa2.setY(2050.0);
- sa2.setWidth(300.0);
- sa2.setHeight(450.0);
- model.addElement(sa2);
- elements.addModelElement(sa2, new CellDesignerGenericProtein("s2"));
-
- Species sa3 = new GenericProtein("sa3");
- sa3.setX(600.0);
- sa3.setY(250.0);
- sa3.setWidth(300.0);
- sa3.setHeight(400.0);
- model.addElement(sa3);
- elements.addModelElement(sa3, new CellDesignerGenericProtein("s3"));
-
- Species sa4 = new GenericProtein("sa4");
- sa4.setX(550.0);
- sa4.setY(350.0);
- sa4.setWidth(300.0);
- sa4.setHeight(450.0);
- model.addElement(sa4);
- elements.addElement(new CellDesignerGenericProtein("s4"));
-
- Species sa5 = new GenericProtein("sa5");
- sa5.setX(10.0);
- sa5.setY(250.0);
- sa5.setWidth(300.0);
- sa5.setHeight(450.0);
- model.addElement(sa5);
- elements.addElement(new CellDesignerGenericProtein("s5"));
-
- Species sa6 = new GenericProtein("sa6");
- sa6.setX(10.0);
- sa6.setY(250.0);
- sa6.setWidth(300.0);
- sa6.setHeight(450.0);
- model.addElement(sa6);
-
- elements.addElement(new CellDesignerGenericProtein("s6"));
-
- Species sa10 = new GenericProtein("sa10");
- sa10.setX(210.0);
- sa10.setY(220.0);
- sa10.setWidth(320.0);
- sa10.setHeight(250.0);
- model.addElement(sa10);
- elements.addElement(new CellDesignerGenericProtein("s10"));
-
- Species sa11 = new GenericProtein("sa11");
- sa11.setX(11.0);
- sa11.setY(320.0);
- sa11.setWidth(321.0);
- sa11.setHeight(150.0);
- model.addElement(sa11);
- elements.addElement(new CellDesignerGenericProtein("s11"));
-
- Species sa12 = new GenericProtein("sa12");
- sa12.setX(12.0);
- sa12.setY(20.0);
- sa12.setWidth(321.0);
- sa12.setHeight(150.0);
- model.addElement(sa12);
- elements.addElement(new CellDesignerGenericProtein("s12"));
-
- Species sa13 = new GenericProtein("sa13");
- sa13.setX(513.0);
- sa13.setY(20.0);
- sa13.setWidth(321.0);
- sa13.setHeight(150.0);
- model.addElement(sa13);
- elements.addElement(new CellDesignerGenericProtein("s13"));
-
- Species sa14 = new GenericProtein("sa14");
- sa14.setX(14.0);
- sa14.setY(820.0);
- sa14.setWidth(321.0);
- sa14.setHeight(150.0);
- model.addElement(sa14);
- elements.addElement(new CellDesignerGenericProtein("s14"));
-
- Species sa15 = new GenericProtein("sa15");
- sa15.setX(815.0);
- sa15.setY(620.0);
- sa15.setWidth(321.0);
- sa15.setHeight(150.0);
- model.addElement(sa15);
- elements.addElement(new CellDesignerGenericProtein("s15"));
-
- return model;
- }
-
- @Test
- public void testLogiGateAndReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateAnd.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof AndOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
-
- model.setName(null);
- String xmlString = cellDesignerXmlParser.toXml(model);
-
- ByteArrayInputStream bais = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
- Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(bais).sizeAutoAdjust(false));
-
- ModelComparator mc = new ModelComparator();
- assertEquals("After CellDesigner xml serialization models are different", 0, mc.compare(model, model2));
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogiGateOrReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateOr.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof OrOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogiGateNotReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateNot.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof NandOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testLogiGateUnknownReaction() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/reactions/logicGateUnknown.xml");
- assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
- assertTrue(reaction instanceof BooleanLogicGateReaction);
- assertEquals(1, reaction.getOperators().size());
- assertTrue(reaction.getOperators().get(0) instanceof UnknownOperator);
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
-
- assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
- assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
-
- // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
- // 1024, 1024, model, true, false, 0, false);
- // generator.saveToPNG("tmp.png");
- // Desktop.getDesktop().open(new File("tmp.png"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProblematicDrawing() throws Exception {
- Model model;
- try {
- model = getModelForFile("testFiles/problematic/reaction_drawing_problem.xml");
- Reaction reaction = model.getReactionByReactionId("re1");
- assertEquals(0, reaction.getCenterPoint().distance(new Point2D.Double(258.5, 145.0)), EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProteinsInsideComplex() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic/proteins_inside_complex.xml");
- for (Element el : model.getElements()) {
- assertFalse(el.getClass().equals(Protein.class));
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ private Logger logger = Logger.getLogger(ReactionParserTests.class.getName());;
+ ReactionXmlParser parser;
+ CellDesignerElementCollection elements;
+
+ @Before
+ public void setUp() throws Exception {
+ elements = new CellDesignerElementCollection();
+
+ parser = new ReactionXmlParser(elements, false);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testColorReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/colorfull_reaction.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ PolylineData line = reaction.getReactants().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+ line = reaction.getProducts().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+ line = reaction.getModifiers().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+ line = reaction.getOperators().get(0).getLine();
+ assertFalse(
+ "000".equals(line.getColor().getRed() + "" + line.getColor().getGreen() + "" + line.getColor().getBlue()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testMissingLines() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/pd_map_with_problematic_reaction_line.xml");
+ assertTrue(model.getElementByElementId("sa5003") instanceof GenericProtein);
+ Set<Reaction> list = model.getReactions();
+ for (Reaction reaction : list) {
+ // reaction re1607 in this model was problematic, but in fact the
+ // problem
+ // can be in any reaction line
+ // if (reaction.getId().equals("re1607")) {
+ List<Line2D> lines = reaction.getLines();
+ for (Line2D line2d : lines) {
+ assertFalse(Double.isNaN(line2d.getX1()));
+ assertFalse(Double.isNaN(line2d.getX2()));
+ assertFalse(Double.isNaN(line2d.getY1()));
+ assertFalse(Double.isNaN(line2d.getY2()));
+ }
+ // }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transition.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+
+ assertTrue(reaction.isReversible());
+ assertEquals(ArrowType.FULL, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(3, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(2, product.getLine().getLines().size());
+
+ assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCenterLineInSimpleReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transition.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ Reactant reactant = reaction.getReactants().get(0);
+
+ Product product = reaction.getProducts().get(0);
+
+ // center of the line should be different than edge points of
+ // reactant/product description
+ assertFalse(reaction.getCenterLine().getP1().distance(reactant.getLine().getEndPoint()) < 1e-6);
+ assertFalse(reaction.getCenterLine().getP2().distance(product.getLine().getBeginPoint()) < 1e-6);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransition2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transitionWithAdditionalNodes.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(2, reaction.getOperators().size());
+ for (Reactant reactant : reaction.getReactants()) {
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+
+ assertTrue(
+ reactant.getLine().getEndPoint().distance(reaction.getReactants().get(0).getLine().getEndPoint()) < 1e-6);
+ }
+
+ for (Product product : reaction.getProducts()) {
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+
+ assertTrue(
+ product.getLine().getBeginPoint().distance(reaction.getProducts().get(0).getLine().getBeginPoint()) < 1e-6);
+ }
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransiotionOmitted() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transition_omitted.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(0, reaction.getOperators().size());
+ assertEquals(KnownTransitionOmittedReaction.class, reaction.getClass());
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownTransition() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/unknown_transition.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscription() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transcription.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TranscriptionReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
+ assertEquals(1, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertTrue(reactant.getLine().getEndPoint().distance(product.getLine().getPoints().get(0)) < 20);
+ assertNotNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscription2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transcription_with_additions.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TranscriptionReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(LineType.DASH_DOT_DOT, reactant.getLine().getType());
+ assertEquals(1, reactant.getLine().getLines().size());
+ NodeOperator operator = null;
+ for (NodeOperator operator2 : reaction.getOperators()) {
+ if (operator2 instanceof SplitOperator)
+ operator = operator2;
+ }
+ assertEquals(LineType.DASH_DOT_DOT, operator.getLine().getType());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranslation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/translation.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TranslationReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(LineType.DASH_DOT, reactant.getLine().getType());
+ assertEquals(1, reactant.getLine().getLines().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.DASH_DOT, operator.getLine().getType());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransport() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/transport.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TransportReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(1, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL_CROSSBAR, product.getLine().getEndAtd().getArrowType());
+ assertEquals(1, product.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHeterodimer() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/heterodimer.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof HeterodimerAssociationReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+ reactant = reaction.getReactants().get(1);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(3, reactant.getLine().getLines().size());
+
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(3, product.getLine().getLines().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(7, operator.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testHeterodimerWithAdditions() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/heterodimerWithAdditions.xml");
+
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof HeterodimerAssociationReaction);
+ assertEquals(3, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+ reactant = reaction.getReactants().get(1);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(3, reactant.getLine().getLines().size());
+
+ for (Product product : reaction.getProducts()) {
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ }
+
+ assertEquals(3, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(7, operator.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDissociation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/dissociation.xml");
+ assertEquals(2, model.getReactions().size());
+ Reaction reaction = null;
+ for (Reaction reaction2 : model.getReactions()) {
+ if (reaction2.getIdReaction().equals("re1"))
+ reaction = reaction2;
+ }
+ assertTrue(reaction instanceof DissociationReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+
+ assertEquals(2, reaction.getProducts().size());
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(5, product.getLine().getLines().size());
+ product = reaction.getProducts().get(1);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(4, product.getLine().getLines().size());
+
+ assertEquals(1, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(5, operator.getLine().getLines().size());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testDissociationWithAddition() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/dissociationWithAddition.xml");
+ assertEquals(2, model.getReactions().size());
+ Reaction reaction = null;
+ for (Reaction reaction2 : model.getReactions()) {
+ if (reaction2.getIdReaction().equals("re1"))
+ reaction = reaction2;
+ }
+ assertTrue(reaction instanceof DissociationReaction);
+ assertEquals(2, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+
+ assertEquals(3, reaction.getProducts().size());
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(5, product.getLine().getLines().size());
+ product = reaction.getProducts().get(1);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(4, product.getLine().getLines().size());
+
+ assertEquals(3, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(5, operator.getLine().getLines().size());
+ assertEquals(DissociationOperator.class, operator.getClass());
+
+ assertNotNull(reaction.getReactionRect());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncation() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/truncation.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof TruncationReaction);
+ assertEquals(1, reaction.getReactants().size());
+ Reactant reactant = reaction.getReactants().get(0);
+ assertEquals(ArrowType.NONE, reactant.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.NONE, reactant.getLine().getEndAtd().getArrowType());
+ assertEquals(2, reactant.getLine().getLines().size());
+
+ assertEquals(2, reaction.getProducts().size());
+ Product product = reaction.getProducts().get(0);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(3, product.getLine().getLines().size());
+ product = reaction.getProducts().get(1);
+ assertEquals(ArrowType.NONE, product.getLine().getBeginAtd().getArrowType());
+ assertEquals(ArrowType.FULL, product.getLine().getEndAtd().getArrowType());
+ assertEquals(4, product.getLine().getLines().size());
+
+ assertEquals(1, reaction.getOperators().size());
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(LineType.SOLID, operator.getLine().getType());
+ assertEquals(1, operator.getLine().getLines().size());
+ assertEquals(TruncationOperator.class, operator.getClass());
+ assertEquals(reaction.getReactionRect(), ReactionRect.RECT_BOLT);
+
+ assertNotNull(reaction.getReactionRect());
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncationWithModifier() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/truncationWithModifier.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ Modifier m = reaction.getModifiers().get(0);
+ assertEquals(ArrowType.CIRCLE, m.getLine().getEndAtd().getArrowType());
+
+ m = reaction.getModifiers().get(1);
+ assertEquals(ArrowType.CROSSBAR, m.getLine().getEndAtd().getArrowType());
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier1() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier1.xml");
+
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(AndOperator.class, operator.getClass());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier2.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(OrOperator.class, operator.getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier3() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier3.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(NandOperator.class, operator.getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifier4() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier4.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getModifiers().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertTrue(operator.isModifierOperator());
+ assertEquals(UnknownOperator.class, operator.getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexReaction.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(0, reaction.getModifiers().size());
+ assertEquals(2, reaction.getOperators().size());
+ assertEquals(2, reaction.getProducts().size());
+ assertEquals(2, reaction.getReactants().size());
+
+ NodeOperator operator = reaction.getOperators().iterator().next();
+ assertEquals(AndOperator.class, operator.getClass());
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0,false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testComplexModifiers5() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexModifier5.xml");
+
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(4, reaction.getModifiers().size());
+ assertEquals(1, reaction.getOperators().size());
+ assertEquals(2, reaction.getOperators().iterator().next().getInputs().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchors() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/problemWithAnchors2.xml");
+
+ Reaction reaction1 = null;
+ Reaction reaction2 = null;
+ for (Reaction reaction : model.getReactions()) {
+ if (reaction.getIdReaction().equals("re2"))
+ reaction1 = reaction;
+ if (reaction.getIdReaction().equals("re3"))
+ reaction2 = reaction;
+ }
+ Reactant reactant = reaction1.getReactants().get(0);
+ Element alias1 = reaction1.getReactants().get(0).getElement();
+ Element alias2 = reaction1.getProducts().get(0).getElement();
+ Product product = reaction1.getProducts().get(0);
+ Point2D point = new Point2D.Double(alias1.getX() + alias1.getWidth() / 2, alias1.getY() + alias1.getHeight());
+ Point2D point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
+ assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
+ assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
+
+ reactant = reaction2.getReactants().get(0);
+ alias1 = reaction2.getReactants().get(0).getElement();
+ alias2 = reaction2.getProducts().get(0).getElement();
+ product = reaction2.getProducts().get(0);
+ point = new Point2D.Double(alias1.getX() + alias1.getWidth(), alias1.getY() + alias1.getHeight() / 2);
+ point2 = new Point2D.Double(alias2.getX(), alias2.getY() + alias2.getHeight() / 2);
+ assertTrue(point.distance(reactant.getLine().getPoints().get(0)) < 1);
+ assertTrue(point2.distance(product.getLine().getEndPoint()) < 1);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchors3() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/problemWithAnchors3.xml");
+ Reaction reaction = null;
+ for (Reaction reaction2 : model.getReactions()) {
+ if (reaction2.getIdReaction().equals("re3"))
+ reaction = reaction2;
+ }
+ Point2D point = new Point2D.Double(164.85583789974368, 86.060142902597);
+ Point2D point2 = new Point2D.Double(397.06477630152193, 284.99999999999994);
+
+ assertTrue(point.distance(reaction.getModifiers().get(0).getLine().getPoints().get(0)) < 1);
+ assertTrue(point2.distance(reaction.getModifiers().get(1).getLine().getPoints().get(0)) < 1);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPositiveInfluence() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/positive_influence.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertNull(reaction.getReactionRect());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchors2() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/complexReactionWithModifier.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ assertEquals(reaction.getProducts().get(0).getLine().length(), reaction.getReactants().get(0).getLine().length(),
+ 1e-6);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicAnchorsWithTwoReactantReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/centeredAnchorInModifier.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ Reactant r = null;
+ for (Reactant reactant : reaction.getReactants()) {
+ if (reactant.getElement().getName().equals("s3")) {
+ r = reactant;
+ }
+ }
+ assertNotNull(r);
+ // I think there is still a bug becaue it should work with smaller delta
+ // :)
+ assertEquals(r.getLine().getPoints().get(1).getX(), r.getLine().getPoints().get(2).getX(), 1);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionWithModifiers() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithModifiers.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ List<Modifier> modifiers = reaction.getModifiers();
+ Modifier sa3 = null;
+ Modifier sa4 = null;
+ for (Modifier modifier : modifiers) {
+ if (modifier.getElement().getElementId().equals("sa3")) {
+ sa3 = modifier;
+ }
+ if (modifier.getElement().getElementId().equals("sa4")) {
+ sa4 = modifier;
+ }
+ }
+ assertEquals(sa3.getLine().getPoints().get(0).distance(new Point2D.Double(101.9591678008944, 68.0)), 0, EPSILON);
+ assertEquals(
+ sa3.getLine().getPoints().get(1).distance(new Point2D.Double(101.86750788643532, 112.89589905362774)), 0,
+ EPSILON);
+ assertEquals(
+ sa3.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0,
+ EPSILON);
+
+ assertEquals(sa4.getLine().getPoints().get(0).distance(new Point2D.Double(267.7075561388218, 54.00000000000001)),
+ 0, EPSILON);
+ assertEquals(sa4.getLine().getPoints().get(1).distance(new Point2D.Double(298.3735877669656, 71.67109819284718)),
+ 0, EPSILON);
+ assertEquals(
+ sa4.getLine().getPoints().get(2).distance(new Point2D.Double(190.66666666666666, 117.66666666666667)), 0,
+ EPSILON);
+
+ // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
+ // false).saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionOperatorsWithOperators() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+ NodeOperator operator1 = reaction.getOperators().get(0);
+ NodeOperator operator2 = reaction.getOperators().get(1);
+ NodeOperator operator3 = reaction.getOperators().get(2);
+
+ // new NormalImageGenerator(1, 0, 0, 1024, 1024, model, true, false, 0,
+ // false).saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ assertEquals(operator1.getLine().getPoints().get(0).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+ EPSILON);
+ assertEquals(
+ operator1.getLine().getPoints().get(1).distance(new Point2D.Double(287.97349260719136, 204.40292958328325)),
+ 0, EPSILON);
+ assertEquals(
+ operator1.getLine().getPoints().get(2).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
+ EPSILON);
+
+ assertEquals(
+ operator2.getLine().getPoints().get(0).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
+ EPSILON);
+ assertEquals(
+ operator2.getLine().getPoints().get(1).distance(new Point2D.Double(372.9868291110932, 203.8558964441427)), 0,
+ EPSILON);
+
+ assertEquals(
+ operator3.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)),
+ 0, EPSILON);
+ assertEquals(
+ operator3.getLine().getPoints().get(1).distance(new Point2D.Double(380.9866634960982, 203.80442011470782)), 0,
+ EPSILON);
+
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+
+ assertEquals(
+ product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
+ EPSILON);
+
+ assertEquals(
+ product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(
+ product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
+ EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionProductsWithOperators() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+
+ Product product1 = reaction.getProducts().get(0);
+ Product product2 = reaction.getProducts().get(1);
+
+ assertEquals(
+ product1.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(product1.getLine().getPoints().get(1).distance(new Point2D.Double(466.0, 203.25738697556727)), 0,
+ EPSILON);
+
+ assertEquals(
+ product2.getLine().getPoints().get(0).distance(new Point2D.Double(394.78939704287654, 203.71560401865366)), 0,
+ EPSILON);
+ assertEquals(
+ product2.getLine().getPoints().get(1).distance(new Point2D.Double(452.96894321929705, 107.00000000000001)), 0,
+ EPSILON);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionReactantsWithOperators() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/reactionWithOperators.xml");
+ Reaction reaction = model.getReactions().iterator().next();
+
+ Reactant reactant1 = reaction.getReactants().get(0);
+ Reactant reactant2 = reaction.getReactants().get(1);
+ Reactant reactant3 = reaction.getReactants().get(2);
+
+ assertEquals(
+ reactant1.getLine().getPoints().get(0).distance(new Point2D.Double(112.53618421052632, 167.46381578947367)),
+ 0, EPSILON);
+ assertEquals(reactant1.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+ EPSILON);
+
+ assertEquals(reactant2.getLine().getPoints().get(0).distance(new Point2D.Double(121.0, 242.0)), 0, EPSILON);
+ assertEquals(reactant2.getLine().getPoints().get(1).distance(new Point2D.Double(287.0, 242.00000000000009)), 0,
+ EPSILON);
+
+ assertEquals(
+ reactant3.getLine().getPoints().get(0).distance(new Point2D.Double(116.65392247520951, 72.34607752479052)), 0,
+ EPSILON);
+ assertEquals(
+ reactant3.getLine().getPoints().get(1).distance(new Point2D.Double(359.1840955643148, 203.94471254019686)), 0,
+ EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionReactionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition.xml");
+
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
+ Reactant reactant1 = reaction1.getReactants().get(0);
+ Reactant reactant2 = reaction2.getReactants().get(0);
+ assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
+ assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
+ assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
+
+ Product product1 = reaction1.getProducts().get(0);
+ Product product2 = reaction2.getProducts().get(0);
+ assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
+ assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
+ assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
+
+ assertEquals(reactant1.getLine().getEndPoint().getX(), reactant2.getLine().getEndPoint().getX(), EPSILON);
+ assertEquals(reactant1.getLine().getEndPoint().getY(), reactant2.getLine().getEndPoint().getY(), EPSILON);
+
+ assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
+ assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionWidthAdditionalNodelReactionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
+ Reactant reactant1 = reaction1.getReactants().get(1);
+ Reactant reactant2 = reaction2.getReactants().get(1);
+ assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
+ assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
+ assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
+
+ Product product1 = reaction1.getProducts().get(1);
+ Product product2 = reaction2.getProducts().get(1);
+ assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
+ assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
+ assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
+
+ assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
+ assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
+ assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranslationToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_translation.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getReactants().size(), reaction2.getReactants().size());
+ Reactant reactant1 = reaction1.getReactants().get(1);
+ Reactant reactant2 = reaction2.getReactants().get(1);
+ assertEquals(reactant1.getLine().getBeginAtd().getArrowType(), reactant2.getLine().getBeginAtd().getArrowType());
+ assertEquals(reactant1.getLine().getEndAtd().getArrowType(), reactant2.getLine().getEndAtd().getArrowType());
+ assertEquals(reactant1.getLine().getLines().size(), reactant2.getLine().getLines().size());
+
+ Product product1 = reaction1.getProducts().get(1);
+ Product product2 = reaction2.getProducts().get(1);
+ assertEquals(product1.getLine().getBeginAtd().getArrowType(), product2.getLine().getBeginAtd().getArrowType());
+ assertEquals(product1.getLine().getEndAtd().getArrowType(), product2.getLine().getEndAtd().getArrowType());
+ assertEquals(product1.getLine().getLines().size(), product2.getLine().getLines().size());
+
+ assertTrue(reactant1.getLine().getEndPoint().distance(reactant2.getLine().getEndPoint()) < 1e-6);
+ assertEquals(reaction1.getReactionRect(), reaction2.getReactionRect());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(product1.getLine().getColor(), product2.getLine().getColor());
+ assertEquals(product1.getLine().getWidth(), product2.getLine().getWidth(), 1e-6);
+
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransportToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transport.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ assertEquals(reaction1.getMiriamData().size(), reaction2.getMiriamData().size());
+ assertEquals(reaction1.getNotes().trim(), reaction2.getNotes().trim());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncationToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncation.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTruncationWithModifierToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownTransitionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTransitionOmittedToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscriptionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTranscriptionWithAdditionsToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionWithOperatorsToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_operators.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionWithModifiersToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionPositiveInfluenceToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_positive_influence.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionHeterodimerWithAdditionsToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionHeterodimerToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getNodes().size(), reaction2.getNodes().size());
+
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testOperatorInReactionHeterodimer() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_heterodimer.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+ for (NodeOperator operator : reaction1.getOperators()) {
+ assertTrue(operator instanceof AssociationOperator);
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionDissociationWithAdditionToXml() throws Exception {
+ try {
+ Model model = getModelFilledWithSpecies();
+ String xmlString = readFile("testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml");
+ Node node = getNodeFromXmlString(xmlString);
+ Reaction reaction1 = parser.getReaction(node, model);
+
+ String xmlString2 = parser.toXml(reaction1);
+ assertNotNull(xmlString2);
+ // logger.debug(xmlString2);
+ Node node2 = getNodeFromXmlString(xmlString2);
+ Reaction reaction2 = parser.getReaction(node2, model);
+
+ assertEquals(reaction1.getName(), reaction2.getName());
+ assertNotNull(reaction1.getName());
+ assertFalse(reaction1.getName().trim().equals(""));
+ List<Line2D> lines1 = reaction1.getLines();
+ List<Line2D> lines2 = reaction2.getLines();
+
+ for (int i = 0; i < lines1.size(); i++) {
+ assertEquals(lines1.get(i).getX1(), lines2.get(i).getX1(), 1e-6);
+ assertEquals(lines1.get(i).getX2(), lines2.get(i).getX2(), 1e-6);
+ assertEquals(lines1.get(i).getY1(), lines2.get(i).getY1(), 1e-6);
+ assertEquals(lines1.get(i).getY2(), lines2.get(i).getY2(), 1e-6);
+ }
+ assertEquals(reaction1.getClass(), reaction2.getClass());
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw e;
+ }
+ }
+
+ private Model getModelFilledWithSpecies() {
+ Model model = new ModelFullIndexed(null);
+
+ Species sa1 = new GenericProtein("sa1");
+ sa1.setX(100.0);
+ sa1.setY(200.0);
+ sa1.setWidth(300.0);
+ sa1.setHeight(400.0);
+ model.addElement(sa1);
+ elements.addModelElement(sa1, new CellDesignerGenericProtein("s1"));
+
+ Species sa2 = new GenericProtein("sa2");
+ sa2.setX(1050.0);
+ sa2.setY(2050.0);
+ sa2.setWidth(300.0);
+ sa2.setHeight(450.0);
+ model.addElement(sa2);
+ elements.addModelElement(sa2, new CellDesignerGenericProtein("s2"));
+
+ Species sa3 = new GenericProtein("sa3");
+ sa3.setX(600.0);
+ sa3.setY(250.0);
+ sa3.setWidth(300.0);
+ sa3.setHeight(400.0);
+ model.addElement(sa3);
+ elements.addModelElement(sa3, new CellDesignerGenericProtein("s3"));
+
+ Species sa4 = new GenericProtein("sa4");
+ sa4.setX(550.0);
+ sa4.setY(350.0);
+ sa4.setWidth(300.0);
+ sa4.setHeight(450.0);
+ model.addElement(sa4);
+ elements.addElement(new CellDesignerGenericProtein("s4"));
+
+ Species sa5 = new GenericProtein("sa5");
+ sa5.setX(10.0);
+ sa5.setY(250.0);
+ sa5.setWidth(300.0);
+ sa5.setHeight(450.0);
+ model.addElement(sa5);
+ elements.addElement(new CellDesignerGenericProtein("s5"));
+
+ Species sa6 = new GenericProtein("sa6");
+ sa6.setX(10.0);
+ sa6.setY(250.0);
+ sa6.setWidth(300.0);
+ sa6.setHeight(450.0);
+ model.addElement(sa6);
+
+ elements.addElement(new CellDesignerGenericProtein("s6"));
+
+ Species sa10 = new GenericProtein("sa10");
+ sa10.setX(210.0);
+ sa10.setY(220.0);
+ sa10.setWidth(320.0);
+ sa10.setHeight(250.0);
+ model.addElement(sa10);
+ elements.addElement(new CellDesignerGenericProtein("s10"));
+
+ Species sa11 = new GenericProtein("sa11");
+ sa11.setX(11.0);
+ sa11.setY(320.0);
+ sa11.setWidth(321.0);
+ sa11.setHeight(150.0);
+ model.addElement(sa11);
+ elements.addElement(new CellDesignerGenericProtein("s11"));
+
+ Species sa12 = new GenericProtein("sa12");
+ sa12.setX(12.0);
+ sa12.setY(20.0);
+ sa12.setWidth(321.0);
+ sa12.setHeight(150.0);
+ model.addElement(sa12);
+ elements.addElement(new CellDesignerGenericProtein("s12"));
+
+ Species sa13 = new GenericProtein("sa13");
+ sa13.setX(513.0);
+ sa13.setY(20.0);
+ sa13.setWidth(321.0);
+ sa13.setHeight(150.0);
+ model.addElement(sa13);
+ elements.addElement(new CellDesignerGenericProtein("s13"));
+
+ Species sa14 = new GenericProtein("sa14");
+ sa14.setX(14.0);
+ sa14.setY(820.0);
+ sa14.setWidth(321.0);
+ sa14.setHeight(150.0);
+ model.addElement(sa14);
+ elements.addElement(new CellDesignerGenericProtein("s14"));
+
+ Species sa15 = new GenericProtein("sa15");
+ sa15.setX(815.0);
+ sa15.setY(620.0);
+ sa15.setWidth(321.0);
+ sa15.setHeight(150.0);
+ model.addElement(sa15);
+ elements.addElement(new CellDesignerGenericProtein("s15"));
+
+ return model;
+ }
+
+ @Test
+ public void testLogiGateAndReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateAnd.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof AndOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ CellDesignerXmlParser cellDesignerXmlParser = new CellDesignerXmlParser();
+
+ model.setName(null);
+ String xmlString = cellDesignerXmlParser.toXml(model);
+
+ ByteArrayInputStream bais = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+ Model model2 = cellDesignerXmlParser.createModel(new ConverterParams().inputStream(bais).sizeAutoAdjust(false));
+
+ ModelComparator mc = new ModelComparator();
+ assertEquals("After CellDesigner xml serialization models are different", 0, mc.compare(model, model2));
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogiGateOrReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateOr.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof OrOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogiGateNotReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateNot.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof NandOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testLogiGateUnknownReaction() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/reactions/logicGateUnknown.xml");
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ assertTrue(reaction instanceof BooleanLogicGateReaction);
+ assertEquals(1, reaction.getOperators().size());
+ assertTrue(reaction.getOperators().get(0) instanceof UnknownOperator);
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
+
+ assertEquals(0.0, reaction.getReactants().get(0).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getReactants().get(1).getLine().getEndPoint().distance(200.0, 127.0), EPSILON);
+ assertEquals(0.0, reaction.getProducts().get(0).getLine().getBeginPoint().distance(200.0, 127.0), EPSILON);
+
+ // NormalImageGenerator generator = new NormalImageGenerator(1, 0, 0,
+ // 1024, 1024, model, true, false, 0, false);
+ // generator.saveToPNG("tmp.png");
+ // Desktop.getDesktop().open(new File("tmp.png"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProblematicDrawing() throws Exception {
+ Model model;
+ try {
+ model = getModelForFile("testFiles/problematic/reaction_drawing_problem.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertEquals(0, reaction.getCenterPoint().distance(new Point2D.Double(258.5, 145.0)), EPSILON);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProteinsInsideComplex() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic/proteins_inside_complex.xml");
+ for (Element el : model.getElements()) {
+ assertFalse(el.getClass().equals(Protein.class));
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testKinetcs() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions/kinetics.xml");
+ Reaction reaction = model.getReactionByReactionId("re1");
+ assertNotNull(reaction.getKinetics());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/testFiles/kinetics/math_using_one_element.xml b/converter-CellDesigner/testFiles/kinetics/math_using_one_element.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0baf8cdf3d070a5c16b9616b0e3d7d30d1d79055
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/math_using_one_element.xml
@@ -0,0 +1,10 @@
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s1 </ci>
+</apply>
+</math>
+</kineticLaw>
diff --git a/converter-CellDesigner/testFiles/kinetics/simple.xml b/converter-CellDesigner/testFiles/kinetics/simple.xml
new file mode 100644
index 0000000000000000000000000000000000000000..04b70999ab504be90ce14cf4a0ceea1310020ed0
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/simple.xml
@@ -0,0 +1,10 @@
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>
diff --git a/converter-CellDesigner/testFiles/kinetics/with_function.xml b/converter-CellDesigner/testFiles/kinetics/with_function.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5bf367b2ce89c1a4f3a787fa8d73427bf8671bec
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/with_function.xml
@@ -0,0 +1,10 @@
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> fun </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>
diff --git a/converter-CellDesigner/testFiles/kinetics/with_global_parameter.xml b/converter-CellDesigner/testFiles/kinetics/with_global_parameter.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6d30ed0d2b54c9823e52e463825e1912bc2535ef
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/with_global_parameter.xml
@@ -0,0 +1,10 @@
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> k1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>
diff --git a/converter-CellDesigner/testFiles/kinetics/with_parameter.xml b/converter-CellDesigner/testFiles/kinetics/with_parameter.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a41be8921785734fc1678d55df9b9fc46fcb4d29
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/with_parameter.xml
@@ -0,0 +1,13 @@
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+<listOfParameters>
+<parameter metaid="k2" id="k2" name="local param" value="0" units="substance"/>
+</listOfParameters>
+</kineticLaw>
diff --git a/converter-CellDesigner/testFiles/kinetics/with_used_parameter.xml b/converter-CellDesigner/testFiles/kinetics/with_used_parameter.xml
new file mode 100644
index 0000000000000000000000000000000000000000..2d6c40edec115a8f086cd550eadb825c435698ba
--- /dev/null
+++ b/converter-CellDesigner/testFiles/kinetics/with_used_parameter.xml
@@ -0,0 +1,13 @@
+<kineticLaw metaid="CDMT00003">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> k2 </ci>
+</apply>
+</math>
+<listOfParameters>
+<parameter metaid="k2" id="k2" name="local param" value="0" units="substance"/>
+</listOfParameters>
+</kineticLaw>
diff --git a/converter-CellDesigner/testFiles/reactions/kinetics.xml b/converter-CellDesigner/testFiles/reactions/kinetics.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6402113c49a73f3d03a1cae3412c1d173b163235
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reactions/kinetics.xml
@@ -0,0 +1,170 @@
+<?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:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<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="0.0" y="0.0"/>
+<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="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<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="0.0" y="0.0"/>
+<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="0.0"/>
+<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"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" 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="default" 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:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</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">
+<annotation/>
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+</apply>
+</math>
+</kineticLaw>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlArgument.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlArgument.java
new file mode 100644
index 0000000000000000000000000000000000000000..106cc227f08a6d5c2cba955902d210fe039dcfc9
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlArgument.java
@@ -0,0 +1,5 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+public interface SbmlArgument {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
index f9e067bae5fa6149bd4151b29694fbfc40c80185..4b7a71ad3812c18a195dd0c6d21a8487f314ae2c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunction.java
@@ -28,7 +28,7 @@ import org.hibernate.annotations.IndexColumn;
@Table(name = "sbml_function")
@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
@XmlRootElement
-public class SbmlFunction implements Serializable {
+public class SbmlFunction implements Serializable, SbmlArgument {
/**
* Default class logger.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
new file mode 100644
index 0000000000000000000000000000000000000000..9a4f29f710663a9d7c9a4b2ae05db811ca157649
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
@@ -0,0 +1,145 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Representation of a single SBML function
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "sbml_kinetics")
+@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
+@XmlRootElement
+public class SbmlKinetics implements Serializable {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(SbmlKinetics.class);
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<SbmlParameter> parameters = new HashSet<>();
+
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<SbmlFunction> functions = new HashSet<>();
+
+ private List<Element> elements = new ArrayList<>();
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ @Column(columnDefinition = "TEXT")
+ private String definition;
+
+ public void addParameter(SbmlParameter parameter) {
+ parameters.add(parameter);
+ }
+
+ public Set<SbmlParameter> getParameters() {
+ return parameters;
+ }
+
+ public List<SbmlArgument> getArguments() {
+ List<SbmlArgument> arguments = new ArrayList<>();
+ arguments.addAll(parameters);
+ arguments.addAll(elements);
+ arguments.addAll(functions);
+ return arguments;
+ }
+
+ public void addElement(Element element) {
+ this.elements.add(element);
+ }
+
+ public String getDefinition() {
+ return definition;
+ }
+
+ public void setDefinition(String definition) {
+ this.definition = definition;
+ }
+
+ public void addElements(Set<Element> elements) {
+ for (Element element : elements) {
+ addElement(element);
+ }
+ }
+
+ public void addParameters(Set<SbmlParameter> parameters) {
+ for (SbmlParameter parameter : parameters) {
+ addParameter(parameter);
+ }
+
+ }
+
+ public void addArguments(Set<SbmlArgument> elementsUsedInKinetics) {
+ for (SbmlArgument argument : elementsUsedInKinetics) {
+ addArgument(argument);
+ }
+
+ }
+
+ public void addArgument(SbmlArgument argument) {
+ if (argument instanceof SbmlParameter) {
+ addParameter((SbmlParameter) argument);
+ } else if (argument instanceof SbmlFunction) {
+ addFunction((SbmlFunction) argument);
+ } else {
+ addElement((Element) argument);
+ }
+
+ }
+
+ public void addFunction(SbmlFunction argument) {
+ functions.add(argument);
+ }
+
+ public SbmlParameter getParameterById(String id) {
+ for (SbmlParameter parameter : parameters) {
+ if (parameter.getParameterId().equals(id)) {
+ return parameter;
+ }
+ }
+ return null;
+ }
+
+ public Set<SbmlFunction> getFunctions() {
+ return functions;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
index 7684fc2f29f15772d4955d440d8442f6ec79e08e..2f8bd963053c1df5867879a4a2f00971a93694ed 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlParameter.java
@@ -22,7 +22,7 @@ import org.apache.log4j.Logger;
@Table(name = "sbml_parameter")
@org.hibernate.annotations.GenericGenerator(name = "test-increment-strategy", strategy = "increment")
@XmlRootElement
-public class SbmlParameter implements Serializable {
+public class SbmlParameter implements Serializable, SbmlArgument {
/**
* Default class logger.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 81ac64e4b5f69d112e7e4233f69db8fa2a7485a8..8a2bb71c2e8b3afdb4e8146548fa511a5fe72864 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -607,4 +608,12 @@ public interface Model {
SbmlUnit getUnitsByUnitId(String unitId);
void addParameters(Collection<SbmlParameter> sbmlParamters);
+
+ void addParameter(SbmlParameter sbmlParameter);
+
+ SbmlParameter getParameterById(String parameterId);
+
+ void addFunction(SbmlFunction sbmlFunction);
+
+ SbmlArgument getFunctionById(String id);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index 3970c18f012b0cc61618d0e30c619f1d92bf95d2..f0644e224121c25051a91224fae3dec166ca94fc 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -774,7 +774,15 @@ public class ModelData implements Serializable {
this.units.add(unit);
}
- public void addParameters(Collection<SbmlParameter> sbmlParamters) {
- this.parameters.addAll(sbmlParamters);
+ public void addParameters(Collection<SbmlParameter> sbmlParameters) {
+ this.parameters.addAll(sbmlParameters);
+ }
+
+ public void addParameter(SbmlParameter sbmlParameter) {
+ this.parameters.add(sbmlParameter);
+ }
+
+ public void addFunction(SbmlFunction sbmlFunction) {
+ this.functions.add(sbmlFunction);
}
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 6cfd3c14a696d8d8821d601bd433571faa646a45..9d32b9e7ace09a41c7705284aa2c0d9c97e20a98 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -18,6 +18,7 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -698,7 +699,37 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void addParameters(Collection<SbmlParameter> sbmlParamters) {
- modelData.addParameters(sbmlParamters);
+ public void addParameters(Collection<SbmlParameter> sbmlParameters) {
+ modelData.addParameters(sbmlParameters);
+ }
+
+ @Override
+ public void addParameter(SbmlParameter sbmlParameter) {
+ modelData.addParameter(sbmlParameter);
+ }
+
+ @Override
+ public SbmlParameter getParameterById(String parameterId) {
+ for (SbmlParameter parameter : getParameters()) {
+ if (parameter.getParameterId().equals(parameterId)) {
+ return parameter;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void addFunction(SbmlFunction sbmlFunction) {
+ modelData.addFunction(sbmlFunction);
+ }
+
+ @Override
+ public SbmlFunction getFunctionById(String functionId) {
+ for (SbmlFunction function : getFunctions()) {
+ if (function.getFunctionId().equals(functionId)) {
+ return function;
+ }
+ }
+ return null;
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index eb6e6ccac3b9756e27a3a55be425cc93dc8a2555..4ce26dd3aae54d82f9ed3d43a2c90e3d35679804 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
@@ -40,6 +40,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.reaction.type.ReactionRect;
@@ -135,11 +136,6 @@ public class Reaction implements BioEntity {
*/
private boolean reversible = false;
- /**
- * Is there a kinetic low describing this reaction.
- */
- private boolean kineticLaw = false;
-
/**
* Symbol of the reaction (RECON).
*/
@@ -212,6 +208,8 @@ public class Reaction implements BioEntity {
@ManyToOne(fetch = FetchType.LAZY)
private ModelData model;
+ private SbmlKinetics kinetics;
+
/**
* Default constructor.
*/
@@ -236,7 +234,6 @@ public class Reaction implements BioEntity {
idReaction = original.getIdReaction();
name = original.getName();
reversible = original.reversible;
- kineticLaw = original.kineticLaw;
miriamDataSet = new HashSet<>();
for (MiriamData md : original.getMiriamData()) {
miriamDataSet.add(new MiriamData(md));
@@ -666,23 +663,6 @@ public class Reaction implements BioEntity {
this.reversible = reversible;
}
- /**
- * @return the kineticLaw
- * @see #kineticLaw
- */
- public boolean isKineticLaw() {
- return kineticLaw;
- }
-
- /**
- * @param kineticLaw
- * the kineticLaw to set
- * @see #kineticLaw
- */
- public void setKineticLaw(boolean kineticLaw) {
- this.kineticLaw = kineticLaw;
- }
-
@Override
public Set<MiriamData> getMiriamData() {
return miriamDataSet;
@@ -889,4 +869,12 @@ public class Reaction implements BioEntity {
}
}
+
+ public SbmlKinetics getKinetics() {
+ return kinetics;
+ }
+
+ public void setKinetics(SbmlKinetics kinetics) {
+ this.kinetics = kinetics;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index 230b8b08dfe9d2a01175d9e1eee87f3e755027e2..78691472086ea094781e84009280198703156401 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -105,11 +105,6 @@ public class ReactionComparator implements Comparator<Reaction> {
return booleanComparator.compare(arg0.isReversible(), arg1.isReversible());
}
- if (booleanComparator.compare(arg0.isKineticLaw(), arg1.isKineticLaw()) != 0) {
- logger.debug("KineticLaw different: " + arg0.isKineticLaw() + ", " + arg1.isKineticLaw());
- return booleanComparator.compare(arg0.isKineticLaw(), arg1.isKineticLaw());
- }
-
if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
logger.debug("Symbol different: " + arg0.getSymbol() + ", " + arg1.getSymbol());
return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
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 a7e4a20b82e8c6306d90ad3b1e7dcc8a5c8235ad..190f1c84fbddd39e0b7d18f7b9436b63713e5807 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
@@ -43,6 +43,7 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.SearchIndex;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMining;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -61,7 +62,7 @@ import lcsb.mapviewer.model.map.model.ModelData;
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(name = "element_type_db", discriminatorType = DiscriminatorType.STRING)
@DiscriminatorValue("GENERIC_ALIAS")
-public abstract class Element implements BioEntity, Serializable {
+public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
*
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
index b699ac87b8b6a7e439ab8ec92892b438bb1d16f2..d97dc565279aadcf3329ea4cc9361fc9c4d7d848 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/AllKineticsTests.java
@@ -5,7 +5,11 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ SbmlFunctionTest.class, SbmlParameterTest.class, SbmlUnitTest.class, SbmlUnitTypeFactorTest.class })
+@SuiteClasses({ SbmlFunctionTest.class, //
+ SbmlKinetics.class, //
+ SbmlParameterTest.class, //
+ SbmlUnitTest.class, //
+ SbmlUnitTypeFactorTest.class })
public class AllKineticsTests {
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..573f9506d1d50d302ac1e2abb31df4f159fefcb1
--- /dev/null
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlKineticsTest.java
@@ -0,0 +1,58 @@
+package lcsb.mapviewer.model.map.kinetics;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import org.junit.Test;
+
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
+public class SbmlKineticsTest {
+
+ @Test
+ public void testAddParameter() {
+ SbmlParameter parameter = new SbmlParameter("");
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addParameter(parameter);
+ assertEquals(kinetics.getParameters().iterator().next(), parameter);
+ }
+
+ @Test
+ public void testAddFunction() {
+ SbmlFunction function = new SbmlFunction("");
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addFunction(function);
+ assertEquals(1, kinetics.getFunctions().size());
+ assertEquals(1, kinetics.getArguments().size());
+ assertEquals(kinetics.getArguments().iterator().next(), function);
+ }
+
+ @Test
+ public void testGetArguments() {
+ SbmlParameter parameter = new SbmlParameter("k1");
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addParameter(parameter);
+ assertTrue(kinetics.getArguments().contains(parameter));
+ }
+
+ @Test
+ public void testAddElement() {
+ Element protein = new GenericProtein("s1");
+
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.addElement(protein);
+ assertEquals(kinetics.getArguments().get(0), protein);
+ }
+
+ @Test
+ public void testSetDefinition() {
+ String definition = "<lambda><bvar><ci> x </ci></bvar></lambda>";
+
+ SbmlKinetics kinetics = new SbmlKinetics();
+ kinetics.setDefinition(definition);
+ assertEquals(definition, kinetics.getDefinition());
+ }
+
+
+}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
index fbd1794bdeb5229886309bb46c3d66ef2f21f415..5f1f3ee27934a0111f3a32147e665a079c21e756 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionComparatorTest.java
@@ -69,13 +69,6 @@ public class ReactionComparatorTest {
reaction1 = createReaction();
reaction2 = createReaction();
- reaction1.setKineticLaw(true);
- assertTrue(comparator.compare(reaction1, reaction2) != 0);
- assertTrue(comparator.compare(reaction2, reaction1) != 0);
-
- reaction1 = createReaction();
- reaction2 = createReaction();
-
reaction1.setSymbol("a");
assertTrue(comparator.compare(reaction1, reaction2) != 0);
assertTrue(comparator.compare(reaction2, reaction1) != 0);
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
index ba848cd6e67581dbfadf02446e4909293ef6c887..aa53199703a30f5f0e014af4166f89aa7cbeed29 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/reaction/ReactionTest.java
@@ -192,8 +192,6 @@ public class ReactionTest extends ModelTestFunctions {
reaction1.setId(id);
reaction1.setNodes(nodes);
reaction1.setNotes(notes);
- reaction1.setKineticLaw(kineticLaw);
- assertEquals(kineticLaw, reaction1.isKineticLaw());
reaction1.setModel(model);
assertEquals(model, reaction1.getModel());
reaction1.setModelData(data);
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
index 4eb421f72825deeadc2c337314283ce342af13df..a2a369d7114ec1686ddf67be0b749ebaced353d9 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ExporterService.java
@@ -611,8 +611,6 @@ public class ExporterService implements IExporterService {
result.append("\t");
result.append("reversible=" + reaction.isReversible());
result.append("\t");
- result.append("kineticLaw=" + reaction.isKineticLaw());
- result.append("\t");
if (reaction.getMiriamData().size() > 0) {
result.append("REACTION_MIRIAM_DATA");
result.append("\t");