diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index f5c1c9dff2818c09021a62c4e0a2bee838c0dca6..e77b6de595c06d3355045c3ad8a3a7b2efb93bc6 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -145,7 +145,10 @@ public class CellDesignerXmlParser extends Converter {
}
// we ignore metaid - it's useless and obstruct data model
// model.setMetaId(XmlParser.getNodeAttr("metaId", modelNode));
- model.setIdModel(XmlParser.getNodeAttr("id", modelNode));
+ String modelId = XmlParser.getNodeAttr("id", modelNode);
+ if (modelId != null && !modelId.isEmpty()) {
+ model.setIdModel(modelId);
+ }
Node compartmentNode = XmlParser.getNode("listOfCompartments", modelNode.getChildNodes());
if (compartmentNode != null) {
@@ -612,7 +615,11 @@ public class CellDesignerXmlParser extends Converter {
+ "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
// metaid is a string cell designer id, usually it's model id and as far as
// we can tell it's not used at all
- result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
+ result.append("<model ");
+ if (model.getIdModel() != null) {
+ result.append("metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\"");
+ }
+ result.append(">\n");
result.append(unitCollectionXmlParser.toXml(model.getUnits()));
result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
@@ -699,7 +706,8 @@ public class CellDesignerXmlParser extends Converter {
result.append("</celldesigner:extension>\n");
XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
- result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(), model.getCreationDate(), model.getModificationDates()));
+ result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(),
+ model.getCreationDate(), model.getModificationDates()));
result.append("</annotation>\n");
return result.toString();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
index d3ca569b69050d4deee73b9e76e1e0a055f552a4..a44fad8785ef94feef83faaeff904759e69110ff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
@@ -404,4 +404,8 @@ public class Layer implements Serializable {
public void removeLayerText(LayerText toRemove) {
texts.remove(toRemove);
}
+
+ public boolean isEmpty() {
+ return this.getOvals().size() == 0 && this.getRectangles().size() == 0 && this.getTexts().size() == 0 && this.getLines().size()==0;
+ }
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
index 4c5c2beb9c07291d502c01e27d9cb23fb736f2cd..b19db3ef42d6c7a25daa04921adc7e379f133d2c 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/GpmlParser.java
@@ -133,7 +133,7 @@ public class GpmlParser {
* @param node
* xml node where data is stored
* @param graph
- * object where data is sotred
+ * object where data is stored
*/
protected void setSize(Node node, Graph graph) {
Element eElement = (Element) node;
@@ -149,7 +149,7 @@ public class GpmlParser {
* @param groups
* xml nodes
* @param graph
- * object where data is sotred
+ * object where data is stored
* @throws UnknownAttributeValueException
* thrown when there is a problem with xml attributes
*/
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
index 83d50098591ceecf2ee8dcd6a83012c3ce4ca521..f9075260c72c0b7b804f71cac056ad34916098d1 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelContructor.java
@@ -281,6 +281,7 @@ public class ModelContructor {
}
res.addMiriamData(dataNode.getReferences());
+ res.setZ(dataNode.getzOrder());
res.setName(dataNode.getName());
return res;
}
@@ -646,6 +647,7 @@ public class ModelContructor {
reaction.setReversible(mapping.isReversible());
reaction.addMiriamData(interaction.getReferences());
+ reaction.setZ(interaction.getzOrder());
for (String ref : interaction.getBiopaxReferences()) {
BiopaxPublication publication = graph.getBiopaxData().getPublicationByReference(ref);
MiriamData md = biopaxParser.createMiriamData(publication);
@@ -926,9 +928,6 @@ public class ModelContructor {
model.setWidth(graph.getBoardWidth());
model.setHeight(graph.getBoardHeight());
- model.setIdModel("1");
- model.getLayers().add(data.layer);
-
addComplexSpecies(model, graph, data);
addElement(model, graph, data);
putSpeciesIntoComplexes(graph, data);
@@ -965,11 +964,15 @@ public class ModelContructor {
logger.warn("[Biopax, " + references.toString() + "]\tModel annotations are not supported.");
}
+ data.layer.addLayerLines(createLines(graph));
+
+ if (!data.layer.isEmpty()) {
+ model.getLayers().add(data.layer);
+ }
+
assignNamesToComplexes(model);
assignNamesToCompartments(model);
- data.layer.addLayerLines(createLines(graph));
-
putAliasesIntoCompartments(model);
return model;
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
index 5e2c2025253143a039f45df407bd11f28229a8b7..6634a3e9bdbe7c106557479e024a1ca78ef9551f 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/ModelToGPML.java
@@ -44,563 +44,590 @@ import lcsb.mapviewer.wikipathway.utils.Geo;
*/
public class ModelToGPML {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = Logger.getLogger(ModelToGPML.class);
-
- /**
- * Maximum distance between point and line. ???
- */
- private static final double DIS_FOR_LINE = 3.0;
-
- /**
- * This value define margin of the group border. Rectangle border will be
- * resized by this value in every direction.
- */
- private static final int GROUP_RECTANGLE_BORDER_MARGIN = 8;
-
- /**
- * First id value used for generating identifiers during conversion.
- */
- private static final int INITIAL_ID_VALUE = 10000;
-
- /**
- * Counter used for generating identifiers if identifiers aren't provided by
- * the gpml model.
- */
- private int idCounter = INITIAL_ID_VALUE;
-
- /**
- * Maximum distance between point and rectangle. ???
- */
- private static final double DIS_FOR_REP = 9.0;
-
- /**
- * Parser used to convert from/to xml {@link MiriamData} annotations.
- */
- private ReferenceParser referenceParser = new ReferenceParser();
-
- /**
- * Parser used to convert from/to xml (in biopax format) {@link MiriamData}
- * annotations.
- */
- private BiopaxParser biopaxParser = new BiopaxParser();
-
- /**
- * Returns new unique identifier for the model.
- *
- * @return new unique identifier for the model
- */
- private String getNewId() {
- idCounter++;
- return "id" + idCounter;
- }
-
- /**
- * This function returns gpml Species type based on class. If it can not
- * recognize one of (Rna,GeneProduct,Protein,Metabolite) it will throw
- * {@link InvalidArgumentException}.
- *
- * @param species
- * species for which gpml type will be returned
- * @return String - type
- */
- private String getType(Species species) {
- String res = "";
- if (species instanceof AntisenseRna) {
- res = "Rna";
- } else if (species instanceof Rna) {
- res = "Rna";
- } else if (species instanceof Gene) {
- res = "GeneProduct";
- } else if (species instanceof Protein) {
- res = "Protein";
- } else if (species instanceof SimpleMolecule) {
- res = "Metabolite";
- } else if (species instanceof Ion) {
- res = "Metabolite";
- } else if (species instanceof Drug) {
- res = "Metabolite";
- } else if (species instanceof Phenotype) {
- res = "Pathway";
- } else if (species instanceof Unknown) {
- res = "Unknown";
- } else if (species instanceof Degraded) {
- res = "Unknown";
- } else {
- throw new InvalidArgumentException("Unknown class type: " + species.getClass());
- }
-
- return res;
- }
-
- /**
- * Since in pathvisio it is impossible to set the size of group rectangle this
- * function calculates new rectangle for complex based on contents of this
- * complex.
- *
- * @param alias
- * alias for which rectangle border is calculated
- * @return rectangle border for alias
- */
- private Rectangle2D getRectangle(Element alias) {
- Rectangle2D res = null;
-
- if (alias instanceof Complex) {
- Complex ca = (Complex) alias;
- if (ca.getElements().size() == 0) {
- res = (Rectangle2D) ca.getBorder().clone();
- } else {
- res = getRectangle(ca.getElements().get(0));
- for (Element al : ca.getElements()) {
- Rectangle2D.union(res, getRectangle(al), res);
- }
- res = new Rectangle2D.Double(
- res.getX() - GROUP_RECTANGLE_BORDER_MARGIN, res.getY() - GROUP_RECTANGLE_BORDER_MARGIN, res.getWidth() + 2 * GROUP_RECTANGLE_BORDER_MARGIN,
- res.getHeight() + 2 * GROUP_RECTANGLE_BORDER_MARGIN);
- }
- } else if (alias instanceof Species) {
- res = (Rectangle2D) alias.getBorder().clone();
- }
- return res;
- }
-
- /**
- * This function calculates {@link PolylineData} based on start
- * {@link Reactant} and end {@link Product}. If end or start points are to far
- * away from their rectangles new points are added.
- *
- * @param start
- * reactant from which polyline starts
- * @param end
- * product where polyline ends
- * @return {@link PolylineData} between start and end
- */
- private PolylineData getPolyline(Reactant start, Product end) {
- PolylineData res = new PolylineData();
-
- NodeOperator and = start.getNodeOperatorForInput();
- // NodeOperator split = end.getNodeOperatorForOutput();
-
- PolylineData startLine = start.getLine();
- Point2D ps = startLine.getBeginPoint();
- Rectangle2D rec1 = getRectangle(start.getElement());
- double dis1 = Geo.distance(ps, rec1);
-
- if (dis1 > DIS_FOR_REP) {
- res.addPoint(Geo.closestPointOnRectangle(rec1, ps));
- }
- for (Point2D p2d : startLine.getPoints()) {
- res.addPoint(p2d);
- }
- if (and != null) {
- for (Point2D p2d : and.getLine().getPoints()) {
- res.addPoint(p2d);
- }
- }
-
- PolylineData endLine = end.getLine();
- Point2D pe = endLine.getEndPoint();
- Rectangle2D rec2 = getRectangle(end.getElement());
- double dis2 = Geo.distance(pe, rec2);
-
- for (Point2D p2d : endLine.getPoints()) {
- res.addPoint(p2d);
- }
- if (dis2 > DIS_FOR_REP) {
- res.addPoint(Geo.closestPointOnRectangle(rec2, pe));
- }
- return Geo.removeRedundantPoints(res);
- }
-
- /**
- * This function calculates PolylineData based on ReactionNode.
- *
- * @param rn
- * rection node for which polyline is calculated
- * @param mainLine
- * main line to which polyline is attached
- * @return polyline for {@link ReactionNode}
- */
- private PolylineData getPolyline(ReactionNode rn, PolylineData mainLine) {
- PolylineData res = new PolylineData();
-
- PolylineData line = rn.getLine();
- Point2D ps = line.getBeginPoint();
- Point2D pe = line.getEndPoint();
- Rectangle2D rec = getRectangle(rn.getElement());
-
- if (rn instanceof Reactant || rn instanceof Modifier) {
- double dis = Geo.distance(ps, rec);
- double dis2 = Geo.distanceFromPolyline(pe, mainLine);
- if (dis > DIS_FOR_REP) {
- res.addPoint(Geo.closestPointOnRectangle(rec, ps));
- }
- for (Point2D p2d : line.getPoints()) {
- res.addPoint(p2d);
- }
- if (dis2 > DIS_FOR_LINE) {
- Point2D tmpPoint = Geo.closestPointOnPolyline(mainLine, pe);
- if (tmpPoint != null) {
- res.addPoint(tmpPoint);
- }
- }
- } else if (rn instanceof Product) {
- double dis = Geo.distance(pe, rec);
- double dis2 = Geo.distanceFromPolyline(ps, mainLine);
- if (dis2 > DIS_FOR_LINE) {
- Point2D tmpPoint = Geo.closestPointOnPolyline(mainLine, ps);
- if (tmpPoint != null) {
- res.addPoint(tmpPoint);
- }
- }
- for (Point2D p2d : line.getPoints()) {
- res.addPoint(p2d);
- }
- if (dis > DIS_FOR_REP) {
- res.addPoint(Geo.closestPointOnRectangle(rec, pe));
- }
- }
- return Geo.removeRedundantPoints(res);
- }
-
- /**
- * This function returns all species names that are in given Compartment.
- *
- * @param ca
- * compartment alias
- * @return string with list of species names in a compartment
- */
- private String getAllNames(Compartment ca) {
- StringBuilder res = new StringBuilder("");
- for (Element a : ca.getAllSubElements()) {
- if (a instanceof Species) {
- Species sp = (Species) a;
- res.append(sp.getName() + ";");
- }
- }
- return res.toString();
- }
-
- /**
- * This function transform Compartments into Shapes (Oval or Rectangle) from
- * PathVisio. LineThickness=3.0 and Color=ffcc66. It can be easily changed.
- *
- * @param model
- * model where compartments are placed
- * @return String that encodes all compartments in gpml format
- */
- private String getComparments(Model model) {
- StringBuilder comparments = new StringBuilder("");
- for (Compartment ca : model.getCompartments()) {
-
- double x = ca.getCenterX(), y = ca.getCenterY(), h = ca.getHeight(), w = ca.getWidth();
- String shape;
- if (ca instanceof OvalCompartment) {
- shape = "Oval";
- } else {
- shape = "Rectangle";
- }
-
- comparments.append(" <Shape TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\">\n");
- comparments.append(" <Comment>" + getAllNames(ca) + "</Comment>\n");
- comparments.append(" <Attribute Key=\"org.pathvisio.CellularComponentProperty\" Value=\"Cell\" />\n");
- comparments.append(" <Attribute Key=\"org.pathvisio.DoubleLineProperty\" Value=\"Double\" />\n");
- comparments.append(
- " <Graphics CenterX=\"" + x + "\" CenterY=\"" + y + "\" Width=\"" + w + "\" Height=\"" + h
- + "\" ZOrder=\"16384\" FontSize=\"20\" Valign=\"Bottom\" ShapeType=\"" + shape
- + "\" LineThickness=\"3.0\" Color=\"ffcc66\" Rotation=\"0.0\" />\n");
- comparments.append(" </Shape>\n");
- }
- return comparments.toString();
- }
-
- /**
- * This function creates Interaction for other product, reactant or modifier
- * from main reaction. This is support function for getInteractions(Model
- * model).
- *
- * @param rn
- * object representing rectanat/product/modifier
- * @param anchId
- * identifier of the anchor where it will be connected
- * @param anchors
- * string builder where anchors are stored (it will be modified to
- * add anchor for this element)
- * @param mainLine
- * line used for connecting this element
- * @return string representing connection of this element to reaction
- * @throws ConverterException
- * thrown when there is a problem with conversion
- */
- private String getInteractionForAnchor(ReactionNode rn, String anchId, StringBuilder anchors, PolylineData mainLine) throws ConverterException {
- StringBuilder interaction = new StringBuilder("");
-
- PolylineData line = getPolyline(rn, mainLine);
- Point2D ps = line.getBeginPoint();
- Point2D pe = line.getEndPoint();
- double anchorPosition = -1;
-
- interaction.append(" <Interaction GraphId=\"" + getNewId() + "\">\n");
- interaction.append(" <Attribute Key=\"org.pathvisio.core.ds\" Value=\"\"/>\n");
- interaction.append(" <Attribute Key=\"org.pathvisio.core.id\" Value=\"\"/>\n");
- interaction.append(" <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
-
- if (rn instanceof Reactant) {
- for (Point2D p2d : line.getPoints()) {
- if (p2d.equals(ps)) {
- interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + rn.getElement().getElementId() + "\"/>\n");
- } else if (p2d.equals(pe)) {
- interaction.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
- } else {
- interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
- }
- }
- } else if (rn instanceof Product) {
- for (Point2D p2d : line.getPoints()) {
- if (p2d.equals(ps)) {
- interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
- } else if (p2d.equals(pe)) {
- interaction.append(
- " <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + rn.getElement().getElementId()
- + "\" ArrowHead=\"mim-conversion\"/>\n");
- } else {
- interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
- }
- }
- } else if (rn instanceof Modifier) {
- for (Point2D p2d : line.getPoints()) {
- if (p2d.equals(ps)) {
- interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + rn.getElement().getElementId() + "\"/>\n");
- } else if (p2d.equals(pe)) {
- interaction.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId + "\" ArrowHead=\"mim-catalysis\"/>\n");
- } else {
- interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
- }
- }
- }
- if (rn instanceof Reactant) {
- anchorPosition = Geo.distanceOnPolyline(mainLine, pe);
- } else if (rn instanceof Product) {
- anchorPosition = Geo.distanceOnPolyline(mainLine, ps);
- } else if (rn instanceof Modifier) {
- anchorPosition = Geo.distanceOnPolyline(mainLine, pe);
- } else {
- throw new InvalidArgumentException("Invalid class type: " + rn.getClass());
- }
- anchors.append(" <Anchor Position=\"" + anchorPosition + "\" Shape=\"None\" GraphId=\"" + anchId + "\"/>\n");
- interaction.append(" </Graphics>\n");
- interaction.append(referenceParser.toXml((MiriamData) null));
- interaction.append(" </Interaction>\n");
-
- return interaction.toString();
- }
-
- /**
- * This function encode SpeciesAliases into DataNodes from .gpml format. Empty
- * complexes are also transformed into DataNodes.
- *
- * @param model
- * model where aliases are placed
- * @return string representing
- * {@link lcsb.mapviewer.wikipathway.model.DataNode data nodes}
- * @throws ConverterException
- * thrown when there is a problem with conversion
- */
- protected String getDataNodes(Model model) throws ConverterException {
- StringBuilder dataNodes = new StringBuilder("");
-
- for (Species sa : model.getNotComplexSpeciesList()) {
- if (!(sa instanceof Complex)) {
- dataNodes.append(" <DataNode TextLabel=\"" + sa.getName() + "\" GraphId=\"" + sa.getElementId() + "\" Type=\"" + getType(sa) + "\"");
- if (sa.getComplex() != null) {
- dataNodes.append(" GroupRef=\"" + sa.getComplex().getElementId() + "\"");
- }
- dataNodes.append(">\n");
-
- dataNodes.append(" <Comment>" + sa.getNotes() + "</Comment>\n");
- dataNodes.append(biopaxParser.toReferenceXml(sa.getMiriamData()));
-
- String red = Integer.toHexString(sa.getColor().getRed());
- String green = Integer.toHexString(sa.getColor().getGreen());
- String blue = Integer.toHexString(sa.getColor().getBlue());
- if (red.length() == 1) {
- red = "0" + red;
- }
- if (green.length() == 1) {
- green = "0" + green;
- }
- if (blue.length() == 1) {
- blue = "0" + blue;
- }
- String color = red + green + blue;
- Rectangle2D rec = sa.getBorder();
-
- dataNodes.append(
- " <Graphics CenterX=\"" + rec.getCenterX() + "\" CenterY=\"" + rec.getCenterY() + "\" Width=\"" + rec.getWidth() + "\" Height=\""
- + rec.getHeight() + "\" ZOrder=\"32883\" FontSize=\"10\" Valign=\"Middle\" Color=\"" + "0000ff" + "\" FillColor=\"" + color + "\"/>\n");
-
- dataNodes.append(referenceParser.toXml(sa.getMiriamData()));
- dataNodes.append(" </DataNode>\n");
- }
- }
-
- /** Special Case for empty Complexes **/
- for (Complex ca : model.getComplexList()) {
- if (ca.getElements().size() == 0) {
- dataNodes.append(" <DataNode TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\" Type=\"Complex\"");
- if (ca.getComplex() != null) {
- dataNodes.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
- }
- dataNodes.append(">\n");
-
- dataNodes.append(biopaxParser.toReferenceXml(ca.getMiriamData()));
- Rectangle2D rec = ca.getBorder();
-
- dataNodes.append(
- " <Graphics CenterX=\"" + rec.getCenterX() + "\" CenterY=\"" + rec.getCenterY() + "\" Width=\"" + rec.getWidth() + "\" Height=\""
- + rec.getHeight() + "\" ZOrder=\"32883\" FontSize=\"10\" Valign=\"Middle\" Color=\"0000ff\" FillColor=\"ffffcc\" LineStyle=\"Broken\"/>\n");
-
- dataNodes.append(referenceParser.toXml(ca.getMiriamData()));
- dataNodes.append(" </DataNode>\n");
- }
- }
-
- return dataNodes.toString();
- }
-
- /**
- * This function encode ComplexAliases into Groups from .gpml format.
- *
- * @param model
- * model where aliases are placed
- * @return string representing groups in gpml format
- */
- protected String getGroups(Model model) {
- StringBuilder groups = new StringBuilder("");
-
- for (Complex ca : model.getComplexList()) {
- if (ca.getElements().size() > 0) {
- groups.append(" <Group GroupId=\"" + ca.getElementId() + "\" GraphId=\"" + ca.getElementId() + "\"");
- if (ca.getComplex() != null) {
- groups.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
- }
- groups.append("/>\n");
- }
- }
- return groups.toString();
- }
-
- /**
- * This function encode Reactions into Interactions from .gpml format.
- *
- * @param model
- * model where reactions are placed
- * @return string with interactions in gpml format
- * @throws ConverterException
- * thrown when there is a problem with conversion
- */
- protected String getInteractions(Model model) throws ConverterException {
- StringBuilder interactions = new StringBuilder("");
- for (Reaction reaction : model.getReactions()) {
-
- StringBuilder anchors = new StringBuilder("");
- StringBuilder tmp = new StringBuilder("");
-
- interactions.append(" <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
- interactions.append(biopaxParser.toReferenceXml(reaction.getMiriamData()));
- // interactions.append(" <Attribute Key=\"org.pathvisio.core.ds\"
- // Value=\"\"/>\n");
- // interactions.append(" <Attribute Key=\"org.pathvisio.core.id\"
- // Value=\"\"/>\n");
- interactions.append(" <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
-
- /** Start and End **/
- Reactant start = reaction.getReactants().get(0);
- Product end = reaction.getProducts().get(0);
-
- PolylineData line = getPolyline(start, end);
- Point2D ps = line.getBeginPoint();
- Point2D pe = line.getEndPoint();
- String sid = start.getElement().getElementId();
- String eid = end.getElement().getElementId();
-
- for (Point2D p2d : line.getPoints()) {
- if (p2d.equals(ps)) {
- interactions.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + sid + "\"/>\n");
- } else if (p2d.equals(pe)) {
- interactions.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + eid + "\" ArrowHead=\"mim-conversion\"/>\n");
- } else {
- interactions.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
- }
- }
- /** Reactants **/
- boolean first = true;
- for (Reactant reactant : reaction.getReactants()) {
- if (first) {
- first = false;
- } else {
- tmp.append(getInteractionForAnchor(reactant, getNewId(), anchors, line));
- }
- }
- /** Products **/
- first = true;
- for (Product product : reaction.getProducts()) {
- if (first) {
- first = false;
- } else {
- tmp.append(getInteractionForAnchor(product, getNewId(), anchors, line));
- }
- }
- /** Modifiers **/
- for (Modifier modifier : reaction.getModifiers()) {
- tmp.append(getInteractionForAnchor(modifier, getNewId(), anchors, line));
- }
-
- interactions.append(anchors.toString());
- interactions.append(" </Graphics>\n");
- interactions.append(referenceParser.toXml(reaction.getMiriamData()));
- interactions.append(" </Interaction>\n");
- interactions.append(tmp.toString());
- }
-
- return interactions.toString();
- }
-
- /**
- * This function returns Model in .gpml format.
- *
- * @param model
- * model to transform
- * @return string in gpml format representing model
- * @throws ConverterException
- * thrown when there is a problem with conversion
- */
- public String getGPML(Model model) throws ConverterException {
-
- StringBuilder gpml = new StringBuilder("");
- gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
- gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\" Name=\"Generated\">\n");
- gpml.append(" <Graphics BoardWidth=\"" + model.getWidth() + "\" BoardHeight=\"" + model.getHeight() + "\"/>\n");
-
- gpml.append(getDataNodes(model));
- String groups = getGroups(model);
- gpml.append(getInteractions(model));
- gpml.append(getComparments(model));
- gpml.append(groups);
- Set<MiriamData> set = new HashSet<>();
- for (BioEntity element : model.getBioEntities()) {
- set.addAll(element.getMiriamData());
- }
-
- // the order here is important...
- gpml.append(" <InfoBox CenterX=\"0.0\" CenterY=\"0.0\"/>\n");
- gpml.append(biopaxParser.toXml(set));
-
- gpml.append("</Pathway>");
-
- return gpml.toString();
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private final Logger logger = Logger.getLogger(ModelToGPML.class);
+
+ /**
+ * Maximum distance between point and line. ???
+ */
+ private static final double DIS_FOR_LINE = 3.0;
+
+ /**
+ * This value define margin of the group border. Rectangle border will be
+ * resized by this value in every direction.
+ */
+ private static final int GROUP_RECTANGLE_BORDER_MARGIN = 8;
+
+ /**
+ * First id value used for generating identifiers during conversion.
+ */
+ private static final int INITIAL_ID_VALUE = 10000;
+
+ /**
+ * Counter used for generating identifiers if identifiers aren't provided by the
+ * gpml model.
+ */
+ private int idCounter = INITIAL_ID_VALUE;
+
+ /**
+ * Maximum distance between point and rectangle. ???
+ */
+ private static final double DIS_FOR_REP = 9.0;
+
+ /**
+ * Parser used to convert from/to xml {@link MiriamData} annotations.
+ */
+ private ReferenceParser referenceParser = new ReferenceParser();
+
+ /**
+ * Parser used to convert from/to xml (in biopax format) {@link MiriamData}
+ * annotations.
+ */
+ private BiopaxParser biopaxParser = new BiopaxParser();
+
+ /**
+ * Returns new unique identifier for the model.
+ *
+ * @return new unique identifier for the model
+ */
+ private String getNewId() {
+ idCounter++;
+ return "id" + idCounter;
+ }
+
+ /**
+ * This function returns gpml Species type based on class. If it can not
+ * recognize one of (Rna,GeneProduct,Protein,Metabolite) it will throw
+ * {@link InvalidArgumentException}.
+ *
+ * @param species
+ * species for which gpml type will be returned
+ * @return String - type
+ */
+ private String getType(Species species) {
+ String res = "";
+ if (species instanceof AntisenseRna) {
+ res = "Rna";
+ } else if (species instanceof Rna) {
+ res = "Rna";
+ } else if (species instanceof Gene) {
+ res = "GeneProduct";
+ } else if (species instanceof Protein) {
+ res = "Protein";
+ } else if (species instanceof SimpleMolecule) {
+ res = "Metabolite";
+ } else if (species instanceof Ion) {
+ res = "Metabolite";
+ } else if (species instanceof Drug) {
+ res = "Metabolite";
+ } else if (species instanceof Phenotype) {
+ res = "Pathway";
+ } else if (species instanceof Unknown) {
+ res = "Unknown";
+ } else if (species instanceof Degraded) {
+ res = "Unknown";
+ } else {
+ throw new InvalidArgumentException("Unknown class type: " + species.getClass());
+ }
+
+ return res;
+ }
+
+ /**
+ * Since in pathvisio it is impossible to set the size of group rectangle this
+ * function calculates new rectangle for complex based on contents of this
+ * complex.
+ *
+ * @param alias
+ * alias for which rectangle border is calculated
+ * @return rectangle border for alias
+ */
+ private Rectangle2D getRectangle(Element alias) {
+ Rectangle2D res = null;
+
+ if (alias instanceof Complex) {
+ Complex ca = (Complex) alias;
+ if (ca.getElements().size() == 0) {
+ res = (Rectangle2D) ca.getBorder().clone();
+ } else {
+ res = getRectangle(ca.getElements().get(0));
+ for (Element al : ca.getElements()) {
+ Rectangle2D.union(res, getRectangle(al), res);
+ }
+ res = new Rectangle2D.Double(
+ res.getX() - GROUP_RECTANGLE_BORDER_MARGIN, res.getY() - GROUP_RECTANGLE_BORDER_MARGIN,
+ res.getWidth() + 2 * GROUP_RECTANGLE_BORDER_MARGIN,
+ res.getHeight() + 2 * GROUP_RECTANGLE_BORDER_MARGIN);
+ }
+ } else if (alias instanceof Species) {
+ res = (Rectangle2D) alias.getBorder().clone();
+ }
+ return res;
+ }
+
+ /**
+ * This function calculates {@link PolylineData} based on start {@link Reactant}
+ * and end {@link Product}. If end or start points are to far away from their
+ * rectangles new points are added.
+ *
+ * @param start
+ * reactant from which polyline starts
+ * @param end
+ * product where polyline ends
+ * @return {@link PolylineData} between start and end
+ */
+ private PolylineData getPolyline(Reactant start, Product end) {
+ PolylineData res = new PolylineData();
+
+ NodeOperator and = start.getNodeOperatorForInput();
+ // NodeOperator split = end.getNodeOperatorForOutput();
+
+ PolylineData startLine = start.getLine();
+ Point2D ps = startLine.getBeginPoint();
+ Rectangle2D rec1 = getRectangle(start.getElement());
+ double dis1 = Geo.distance(ps, rec1);
+
+ if (dis1 > DIS_FOR_REP) {
+ res.addPoint(Geo.closestPointOnRectangle(rec1, ps));
+ }
+ for (Point2D p2d : startLine.getPoints()) {
+ res.addPoint(p2d);
+ }
+ if (and != null) {
+ for (Point2D p2d : and.getLine().getPoints()) {
+ res.addPoint(p2d);
+ }
+ }
+
+ PolylineData endLine = end.getLine();
+ Point2D pe = endLine.getEndPoint();
+ Rectangle2D rec2 = getRectangle(end.getElement());
+ double dis2 = Geo.distance(pe, rec2);
+
+ for (Point2D p2d : endLine.getPoints()) {
+ res.addPoint(p2d);
+ }
+ if (dis2 > DIS_FOR_REP) {
+ res.addPoint(Geo.closestPointOnRectangle(rec2, pe));
+ }
+ return Geo.removeRedundantPoints(res);
+ }
+
+ /**
+ * This function calculates PolylineData based on ReactionNode.
+ *
+ * @param rn
+ * rection node for which polyline is calculated
+ * @param mainLine
+ * main line to which polyline is attached
+ * @return polyline for {@link ReactionNode}
+ */
+ private PolylineData getPolyline(ReactionNode rn, PolylineData mainLine) {
+ PolylineData res = new PolylineData();
+
+ PolylineData line = rn.getLine();
+ Point2D ps = line.getBeginPoint();
+ Point2D pe = line.getEndPoint();
+ Rectangle2D rec = getRectangle(rn.getElement());
+
+ if (rn instanceof Reactant || rn instanceof Modifier) {
+ double dis = Geo.distance(ps, rec);
+ double dis2 = Geo.distanceFromPolyline(pe, mainLine);
+ if (dis > DIS_FOR_REP) {
+ res.addPoint(Geo.closestPointOnRectangle(rec, ps));
+ }
+ for (Point2D p2d : line.getPoints()) {
+ res.addPoint(p2d);
+ }
+ if (dis2 > DIS_FOR_LINE) {
+ Point2D tmpPoint = Geo.closestPointOnPolyline(mainLine, pe);
+ if (tmpPoint != null) {
+ res.addPoint(tmpPoint);
+ }
+ }
+ } else if (rn instanceof Product) {
+ double dis = Geo.distance(pe, rec);
+ double dis2 = Geo.distanceFromPolyline(ps, mainLine);
+ if (dis2 > DIS_FOR_LINE) {
+ Point2D tmpPoint = Geo.closestPointOnPolyline(mainLine, ps);
+ if (tmpPoint != null) {
+ res.addPoint(tmpPoint);
+ }
+ }
+ for (Point2D p2d : line.getPoints()) {
+ res.addPoint(p2d);
+ }
+ if (dis > DIS_FOR_REP) {
+ res.addPoint(Geo.closestPointOnRectangle(rec, pe));
+ }
+ }
+ return Geo.removeRedundantPoints(res);
+ }
+
+ /**
+ * This function returns all species names that are in given Compartment.
+ *
+ * @param ca
+ * compartment alias
+ * @return string with list of species names in a compartment
+ */
+ private String getAllNames(Compartment ca) {
+ StringBuilder res = new StringBuilder("");
+ for (Element a : ca.getAllSubElements()) {
+ if (a instanceof Species) {
+ Species sp = (Species) a;
+ res.append(sp.getName() + ";");
+ }
+ }
+ return res.toString();
+ }
+
+ /**
+ * This function transform Compartments into Shapes (Oval or Rectangle) from
+ * PathVisio. LineThickness=3.0 and Color=ffcc66. It can be easily changed.
+ *
+ * @param model
+ * model where compartments are placed
+ * @return String that encodes all compartments in gpml format
+ */
+ private String getComparments(Model model) {
+ StringBuilder comparments = new StringBuilder("");
+ for (Compartment ca : model.getCompartments()) {
+
+ double x = ca.getCenterX(), y = ca.getCenterY(), h = ca.getHeight(), w = ca.getWidth();
+ String shape;
+ if (ca instanceof OvalCompartment) {
+ shape = "Oval";
+ } else {
+ shape = "Rectangle";
+ }
+
+ comparments.append(" <Shape TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\">\n");
+ comparments.append(" <Comment>" + getAllNames(ca) + "</Comment>\n");
+ comparments.append(" <Attribute Key=\"org.pathvisio.CellularComponentProperty\" Value=\"Cell\" />\n");
+ comparments.append(" <Attribute Key=\"org.pathvisio.DoubleLineProperty\" Value=\"Double\" />\n");
+ comparments.append(
+ " <Graphics CenterX=\"" + x + "\" CenterY=\"" + y + "\" Width=\"" + w + "\" Height=\"" + h
+ + "\" ZOrder=\"" + ca.getZ() + "\" FontSize=\"20\" Valign=\"Bottom\" ShapeType=\"" + shape
+ + "\" LineThickness=\"3.0\" Color=\"ffcc66\" Rotation=\"0.0\" />\n");
+ comparments.append(" </Shape>\n");
+ }
+ return comparments.toString();
+ }
+
+ /**
+ * This function creates Interaction for other product, reactant or modifier
+ * from main reaction. This is support function for getInteractions(Model
+ * model).
+ *
+ * @param rn
+ * object representing rectanat/product/modifier
+ * @param anchId
+ * identifier of the anchor where it will be connected
+ * @param anchors
+ * string builder where anchors are stored (it will be modified to add
+ * anchor for this element)
+ * @param mainLine
+ * line used for connecting this element
+ * @return string representing connection of this element to reaction
+ * @throws ConverterException
+ * thrown when there is a problem with conversion
+ */
+ private String getInteractionForAnchor(ReactionNode rn, String anchId, StringBuilder anchors, PolylineData mainLine)
+ throws ConverterException {
+ StringBuilder interaction = new StringBuilder("");
+
+ PolylineData line = getPolyline(rn, mainLine);
+ Point2D ps = line.getBeginPoint();
+ Point2D pe = line.getEndPoint();
+ double anchorPosition = -1;
+
+ interaction.append(" <Interaction GraphId=\"" + getNewId() + "\">\n");
+ interaction.append(" <Attribute Key=\"org.pathvisio.core.ds\" Value=\"\"/>\n");
+ interaction.append(" <Attribute Key=\"org.pathvisio.core.id\" Value=\"\"/>\n");
+ interaction.append(" <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
+
+ if (rn instanceof Reactant) {
+ for (Point2D p2d : line.getPoints()) {
+ if (p2d.equals(ps)) {
+ interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\""
+ + rn.getElement().getElementId() + "\"/>\n");
+ } else if (p2d.equals(pe)) {
+ interaction
+ .append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
+ } else {
+ interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
+ }
+ }
+ } else if (rn instanceof Product) {
+ for (Point2D p2d : line.getPoints()) {
+ if (p2d.equals(ps)) {
+ interaction
+ .append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + anchId + "\"/>\n");
+ } else if (p2d.equals(pe)) {
+ interaction.append(
+ " <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\""
+ + rn.getElement().getElementId()
+ + "\" ArrowHead=\"mim-conversion\"/>\n");
+ } else {
+ interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
+ }
+ }
+ } else if (rn instanceof Modifier) {
+ for (Point2D p2d : line.getPoints()) {
+ if (p2d.equals(ps)) {
+ interaction.append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\""
+ + rn.getElement().getElementId() + "\"/>\n");
+ } else if (p2d.equals(pe)) {
+ interaction.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + anchId
+ + "\" ArrowHead=\"mim-catalysis\"/>\n");
+ } else {
+ interaction.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
+ }
+ }
+ }
+ if (rn instanceof Reactant) {
+ anchorPosition = Geo.distanceOnPolyline(mainLine, pe);
+ } else if (rn instanceof Product) {
+ anchorPosition = Geo.distanceOnPolyline(mainLine, ps);
+ } else if (rn instanceof Modifier) {
+ anchorPosition = Geo.distanceOnPolyline(mainLine, pe);
+ } else {
+ throw new InvalidArgumentException("Invalid class type: " + rn.getClass());
+ }
+ anchors.append(" <Anchor Position=\"" + anchorPosition + "\" Shape=\"None\" GraphId=\"" + anchId + "\"/>\n");
+ interaction.append(" </Graphics>\n");
+ interaction.append(referenceParser.toXml((MiriamData) null));
+ interaction.append(" </Interaction>\n");
+
+ return interaction.toString();
+ }
+
+ /**
+ * This function encode SpeciesAliases into DataNodes from .gpml format. Empty
+ * complexes are also transformed into DataNodes.
+ *
+ * @param model
+ * model where aliases are placed
+ * @return string representing {@link lcsb.mapviewer.wikipathway.model.DataNode
+ * data nodes}
+ * @throws ConverterException
+ * thrown when there is a problem with conversion
+ */
+ protected String getDataNodes(Model model) throws ConverterException {
+ StringBuilder dataNodes = new StringBuilder("");
+
+ for (Species sa : model.getNotComplexSpeciesList()) {
+ if (!(sa instanceof Complex)) {
+ dataNodes.append(" <DataNode TextLabel=\"" + sa.getName() + "\" GraphId=\"" + sa.getElementId() + "\" Type=\""
+ + getType(sa) + "\"");
+ if (sa.getComplex() != null) {
+ dataNodes.append(" GroupRef=\"" + sa.getComplex().getElementId() + "\"");
+ }
+ dataNodes.append(">\n");
+
+ dataNodes.append(" <Comment>" + sa.getNotes() + "</Comment>\n");
+ dataNodes.append(biopaxParser.toReferenceXml(sa.getMiriamData()));
+
+ String red = Integer.toHexString(sa.getColor().getRed());
+ String green = Integer.toHexString(sa.getColor().getGreen());
+ String blue = Integer.toHexString(sa.getColor().getBlue());
+ if (red.length() == 1) {
+ red = "0" + red;
+ }
+ if (green.length() == 1) {
+ green = "0" + green;
+ }
+ if (blue.length() == 1) {
+ blue = "0" + blue;
+ }
+ String color = red + green + blue;
+ Rectangle2D rec = sa.getBorder();
+
+ dataNodes.append(
+ " <Graphics CenterX=\"" + rec.getCenterX() +
+ "\" CenterY=\"" + rec.getCenterY() +
+ "\" Width=\"" + rec.getWidth() +
+ "\" Height=\"" + rec.getHeight() +
+ "\" ZOrder=\"" + sa.getZ() +
+ "\" FontSize=\"10\"" +
+ " Valign=\"Middle\" "
+ + "Color=\"" + "0000ff"
+ + "\" FillColor=\"" + color + "\"/>\n");
+
+ dataNodes.append(referenceParser.toXml(sa.getMiriamData()));
+ dataNodes.append(" </DataNode>\n");
+ }
+ }
+
+ /** Special Case for empty Complexes **/
+ for (Complex ca : model.getComplexList()) {
+ if (ca.getElements().size() == 0) {
+ dataNodes.append(
+ " <DataNode TextLabel=\"" + ca.getName() + "\" GraphId=\"" + ca.getElementId() + "\" Type=\"Complex\"");
+ if (ca.getComplex() != null) {
+ dataNodes.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
+ }
+ dataNodes.append(">\n");
+
+ dataNodes.append(biopaxParser.toReferenceXml(ca.getMiriamData()));
+ Rectangle2D rec = ca.getBorder();
+
+ dataNodes.append(
+ " <Graphics CenterX=\"" + rec.getCenterX() +
+ "\" CenterY=\"" + rec.getCenterY() +
+ "\" Width=\"" + rec.getWidth() +
+ "\" Height=\"" + rec.getHeight() +
+ "\" ZOrder=\"" + ca.getZ() +
+ "\" FontSize=\"10\"" +
+ " Valign=\"Middle\" " +
+ "Color=\"0000ff\" " +
+ "FillColor=\"ffffcc\"" +
+ " LineStyle=\"Broken\"/>\n");
+
+ dataNodes.append(referenceParser.toXml(ca.getMiriamData()));
+ dataNodes.append(" </DataNode>\n");
+ }
+ }
+
+ return dataNodes.toString();
+ }
+
+ /**
+ * This function encode ComplexAliases into Groups from .gpml format.
+ *
+ * @param model
+ * model where aliases are placed
+ * @return string representing groups in gpml format
+ */
+ protected String getGroups(Model model) {
+ StringBuilder groups = new StringBuilder("");
+
+ for (Complex ca : model.getComplexList()) {
+ if (ca.getElements().size() > 0) {
+ groups.append(" <Group GroupId=\"" + ca.getElementId() + "\" GraphId=\"" + ca.getElementId() + "\"");
+ if (ca.getComplex() != null) {
+ groups.append(" GroupRef=\"" + ca.getComplex().getElementId() + "\"");
+ }
+ groups.append("/>\n");
+ }
+ }
+ return groups.toString();
+ }
+
+ /**
+ * This function encode Reactions into Interactions from .gpml format.
+ *
+ * @param model
+ * model where reactions are placed
+ * @return string with interactions in gpml format
+ * @throws ConverterException
+ * thrown when there is a problem with conversion
+ */
+ protected String getInteractions(Model model) throws ConverterException {
+ StringBuilder interactions = new StringBuilder("");
+ for (Reaction reaction : model.getReactions()) {
+
+ StringBuilder anchors = new StringBuilder("");
+ StringBuilder tmp = new StringBuilder("");
+
+ interactions.append(" <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
+ interactions.append(biopaxParser.toReferenceXml(reaction.getMiriamData()));
+ // interactions.append(" <Attribute Key=\"org.pathvisio.core.ds\"
+ // Value=\"\"/>\n");
+ // interactions.append(" <Attribute Key=\"org.pathvisio.core.id\"
+ // Value=\"\"/>\n");
+ interactions.append(" <Graphics ConnectorType=\"Segmented\" ZOrder=\"32827\" LineThickness=\"1.0\">\n");
+
+ /** Start and End **/
+ Reactant start = reaction.getReactants().get(0);
+ Product end = reaction.getProducts().get(0);
+
+ PolylineData line = getPolyline(start, end);
+ Point2D ps = line.getBeginPoint();
+ Point2D pe = line.getEndPoint();
+ String sid = start.getElement().getElementId();
+ String eid = end.getElement().getElementId();
+
+ for (Point2D p2d : line.getPoints()) {
+ if (p2d.equals(ps)) {
+ interactions
+ .append(" <Point X=\"" + ps.getX() + "\" Y=\"" + ps.getY() + "\" GraphRef=\"" + sid + "\"/>\n");
+ } else if (p2d.equals(pe)) {
+ interactions.append(" <Point X=\"" + pe.getX() + "\" Y=\"" + pe.getY() + "\" GraphRef=\"" + eid
+ + "\" ArrowHead=\"mim-conversion\"/>\n");
+ } else {
+ interactions.append(" <Point X=\"" + p2d.getX() + "\" Y=\"" + p2d.getY() + "\"/>\n");
+ }
+ }
+ /** Reactants **/
+ boolean first = true;
+ for (Reactant reactant : reaction.getReactants()) {
+ if (first) {
+ first = false;
+ } else {
+ tmp.append(getInteractionForAnchor(reactant, getNewId(), anchors, line));
+ }
+ }
+ /** Products **/
+ first = true;
+ for (Product product : reaction.getProducts()) {
+ if (first) {
+ first = false;
+ } else {
+ tmp.append(getInteractionForAnchor(product, getNewId(), anchors, line));
+ }
+ }
+ /** Modifiers **/
+ for (Modifier modifier : reaction.getModifiers()) {
+ tmp.append(getInteractionForAnchor(modifier, getNewId(), anchors, line));
+ }
+
+ interactions.append(anchors.toString());
+ interactions.append(" </Graphics>\n");
+ interactions.append(referenceParser.toXml(reaction.getMiriamData()));
+ interactions.append(" </Interaction>\n");
+ interactions.append(tmp.toString());
+ }
+
+ return interactions.toString();
+ }
+
+ /**
+ * This function returns Model in .gpml format.
+ *
+ * @param model
+ * model to transform
+ * @return string in gpml format representing model
+ * @throws ConverterException
+ * thrown when there is a problem with conversion
+ */
+ public String getGPML(Model model) throws ConverterException {
+
+ StringBuilder gpml = new StringBuilder("");
+ gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\" Name=\"Generated\">\n");
+ gpml.append(" <Graphics BoardWidth=\"" + model.getWidth() + "\" BoardHeight=\"" + model.getHeight() + "\"/>\n");
+
+ gpml.append(getDataNodes(model));
+ String groups = getGroups(model);
+ gpml.append(getInteractions(model));
+ gpml.append(getComparments(model));
+ gpml.append(groups);
+ Set<MiriamData> set = new HashSet<>();
+ for (BioEntity element : model.getBioEntities()) {
+ set.addAll(element.getMiriamData());
+ }
+
+ // the order here is important...
+ gpml.append(" <InfoBox CenterX=\"0.0\" CenterY=\"0.0\"/>\n");
+ gpml.append(biopaxParser.toXml(set));
+
+ gpml.append("</Pathway>");
+
+ return gpml.toString();
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
index ae3dccb80a78c2514cf1debb6d2796abd44c0618..7af111468d47235671d1d732c1a51c806b31d728 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ComplexReactionToModelTest.java
@@ -5,12 +5,10 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
import java.awt.Color;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
@@ -18,199 +16,183 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ComplexReactionToModelTest extends WikipathwaysTestFunctions{
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ComplexReactionToModelTest.class);
-
- @Test
- public void ComplexReactionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/two_segment_reaction.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
+public class ComplexReactionToModelTest extends WikipathwaysTestFunctions {
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ComplexReactionToModelTest.class);
- assertEquals(1, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
+ @Test
+ public void ComplexReactionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/two_segment_reaction.gpml";
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void ComplexReactantReactionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/two_reactants_reaction.gpml";
+ assertEquals(1, model1.getReactions().size());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(2, reaction.getReactants().size());
- assertEquals(1, reaction.getProducts().size());
+ @Test
+ public void ComplexReactantReactionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/two_reactants_reaction.gpml";
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void ComplexSplitReactionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/split_two_segment_reaction.gpml";
+ assertEquals(1, model1.getReactions().size());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getReactions().size());
+ assertEquals(2, reaction.getReactants().size());
+ assertEquals(1, reaction.getProducts().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(1, reaction.getReactants().size());
- assertEquals(2, reaction.getProducts().size());
+ @Test
+ public void ComplexSplitReactionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/split_two_segment_reaction.gpml";
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void problematicReactantTest() throws Exception {
- try {
- ModelComparator mc = new ModelComparator(1.0);
+ assertEquals(1, model1.getReactions().size());
- String fileName = "testFiles/small/problematic_reactant.gpml";
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, reaction.getReactants().size());
+ assertEquals(2, reaction.getProducts().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
+ @Test
+ public void problematicReactantTest() throws Exception {
+ try {
+ ModelComparator mc = new ModelComparator(1.0);
- assertEquals(7, getWarnings().size());
+ String fileName = "testFiles/small/problematic_reactant.gpml";
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void problematicReactant2Test() throws Exception {
- try {
- ModelComparator mc = new ModelComparator(1.0);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+ assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- String fileName = "testFiles/small/problematic_reactant_2.gpml";
+ assertEquals(7, getWarnings().size());
- Model model1 = new GPMLToModel().getModel(fileName);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ @Test
+ public void problematicReactant2Test() throws Exception {
+ try {
+ ModelComparator mc = new ModelComparator(1.0);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
- assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
+ String fileName = "testFiles/small/problematic_reactant_2.gpml";
- assertEquals(3, getWarnings().size());
+ Model model1 = new GPMLToModel().getModel(fileName);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+ assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- @Test
- public void missingNodesInReactionTest() throws Exception {
- try {
- ModelComparator mc = new ModelComparator(1.0);
+ assertEquals(3, getWarnings().size());
- String fileName = "testFiles/small/missing_nodes_in_reaction.gpml";
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void missingNodesInReactionTest() throws Exception {
+ try {
+ ModelComparator mc = new ModelComparator(1.0);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ String fileName = "testFiles/small/missing_nodes_in_reaction.gpml";
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
+ assertEquals("File " + fileName + " different after transformation", 0, mc.compare(model1, model2));
- assertEquals(5, getWarnings().size());
+ assertEquals(5, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void testColorReaction() throws Exception {
- try {
- String fileName = "testFiles/small/color_reaction.gpml";
- Model model = new GPMLToModel().getModel(fileName);
+ @Test
+ public void testColorReaction() throws Exception {
+ try {
+ String fileName = "testFiles/small/color_reaction.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
- assertEquals(1, model.getReactions().size());
+ assertEquals(1, model.getReactions().size());
- Reaction reaction = model.getReactions().iterator().next();
+ Reaction reaction = model.getReactions().iterator().next();
- assertFalse(Color.BLACK.equals(reaction.getReactants().get(0).getLine().getColor()));
+ assertFalse(Color.BLACK.equals(reaction.getReactants().get(0).getLine().getColor()));
- Element redAlias = model.getElementByElementId("d9620");
- Element blackAlias = model.getElementByElementId("d046f");
- assertFalse(Color.BLACK.equals(redAlias.getColor()));
- assertTrue(Color.WHITE.equals(blackAlias.getColor()));
+ Element redAlias = model.getElementByElementId("d9620");
+ Element blackAlias = model.getElementByElementId("d046f");
+ assertFalse(Color.BLACK.equals(redAlias.getColor()));
+ assertTrue(Color.WHITE.equals(blackAlias.getColor()));
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- /**
- * @throws Exception
- */
- @Test
- public void testReactionWithTwoSegments() throws Exception {
- try {
- String fileName = "testFiles/small/color_reaction.gpml";
- Model model = new GPMLToModel().getModel(fileName);
+ /**
+ * @throws Exception
+ */
+ @Test
+ public void testReactionWithTwoSegments() throws Exception {
+ try {
+ String fileName = "testFiles/small/color_reaction.gpml";
+ Model model = new GPMLToModel().getModel(fileName);
- Reaction reaction = model.getReactions().iterator().next();
+ Reaction reaction = model.getReactions().iterator().next();
- int lineCount = 0;
- for (AbstractNode node : reaction.getNodes()) {
- lineCount += node.getLine().getLines().size();
- }
+ int lineCount = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ lineCount += node.getLine().getLines().size();
+ }
- assertEquals(4, lineCount);
+ assertEquals(4, lineCount);
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 47b4d62fd8d5d58925f2acdb91c7bd74219210c4..32c31e6da8f88a889581c55b17d527d6f78ded72 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -46,11 +46,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
assertEquals(22, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -68,11 +64,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
assertEquals(22, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -91,11 +83,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
Model model1 = new GPMLToModel().getModel(pathToFile + fileName);
assertEquals(15, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -114,11 +102,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(16, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -137,11 +121,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(3, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -160,11 +140,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(38, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -184,11 +160,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(41, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -208,11 +180,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(22, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -232,12 +200,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -257,12 +220,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -282,12 +240,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -306,12 +259,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(3, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -330,12 +278,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(3, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -476,11 +419,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/compartment/complex_in_compartment.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
@@ -497,11 +436,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/small/reaction_to_complex.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
@@ -518,11 +453,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/reactions/complex_color_reaction.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -537,11 +468,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/reactions/complex_color_reaction2.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -560,11 +487,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertNotNull(protein);
assertEquals(2, protein.getModificationResidues().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2Xml(model1, false);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
@@ -584,11 +507,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertNotNull(protein);
assertEquals(2, protein.getModificationResidues().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2Xml(model1, false);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
@@ -628,11 +547,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(1, model1.getReactions().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -652,11 +567,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
@@ -675,11 +586,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
assertEquals(0, protein.getModificationResidues().size());
assertEquals("GTP", protein.getStructuralState());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
assertEquals(0, mc.compare(model1, model2));
} catch (Exception e) {
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
index 6b293c28e944192141caf1a238718b87e4c1e1d3..f19d4987a2956e1d15ca9c6eaf3e20e9e71a7195 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionElbowsTest.java
@@ -4,872 +4,821 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import java.awt.geom.Line2D;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
-public class ReactionElbowsTest extends WikipathwaysTestFunctions{
- private final static double EPSILON = 1e-6;
+public class ReactionElbowsTest extends WikipathwaysTestFunctions {
+ private final static double EPSILON = 1e-6;
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionElbowsTest.class);
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionElbowsTest.class);
- private ModelComparator mc = new ModelComparator(1.0);
+ private ModelComparator mc = new ModelComparator(1.0);
- @Test
- public void LineReactionNorthToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionNorthToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(5, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionNorthToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionNorthToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionNorthToEast2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_e_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionNorthToEast2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_e_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionNorthToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionNorthToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(7, lines);
+ assertEquals(7, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionNorthToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionNorthToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ logger.debug(model1.getIdModel());
+ logger.debug(model2.getIdModel());
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionNorthToWest2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_n_w_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionNorthToWest2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_n_w_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionEastToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionEastToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionEastToNorth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_n_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionEastToNorth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_n_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionEastToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionEastToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(5, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionEastToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionEastToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionEastToSouth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_s_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionEastToSouth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_s_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionEastToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_e_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionEastToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_e_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(5, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionSouthToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionSouthToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(5, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionSouthToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionSouthToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionSouthToEast2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_e_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionSouthToEast2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_e_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionSouthToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionSouthToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(5, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionSouthToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionSouthToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionSouthToWest2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_s_w_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionSouthToWest2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_s_w_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionWestToNorth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_n.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionWestToNorth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_n.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionWestToNorth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_n_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionWestToNorth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_n_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionWestToEast() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_e.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionWestToEast() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_e.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(7, lines);
+ assertEquals(7, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionWestToSouth() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_s.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionWestToSouth() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_s.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(6, lines);
+ assertEquals(6, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionWestToSouth2() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_s_2.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionWestToSouth2() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_s_2.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(4, lines);
+ assertEquals(4, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void LineReactionWestToWest() throws Exception {
- try {
- String fileName = "testFiles/elbow/elbow_line_w_w.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void LineReactionWestToWest() throws Exception {
+ try {
+ String fileName = "testFiles/elbow/elbow_line_w_w.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- int lines = 0;
- for (AbstractNode node : reaction.getNodes()) {
- for (Line2D line : node.getLine().getLines()) {
- assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(), isHvLine(line));
- lines++;
- }
- }
+ int lines = 0;
+ for (AbstractNode node : reaction.getNodes()) {
+ for (Line2D line : node.getLine().getLines()) {
+ assertTrue("Lines should be horizontal or vertical, but found: " + line.getP1() + " - " + line.getP2(),
+ isHvLine(line));
+ lines++;
+ }
+ }
- assertEquals(5, lines);
+ assertEquals(5, lines);
- assertEquals(1, getWarnings().size());
+ assertEquals(1, getWarnings().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
+ assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- private boolean isHvLine(Line2D line) {
- return Math.abs(line.getX1() - line.getX2()) < EPSILON || Math.abs(line.getY1() - line.getY2()) < EPSILON;
- }
+ private boolean isHvLine(Line2D line) {
+ return Math.abs(line.getX1() - line.getX2()) < EPSILON || Math.abs(line.getY1() - line.getY2()) < EPSILON;
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
index 25e05d27f6ec478569112ab3894ca1b31d95c1d5..0d529b8fbe96a0a0a2946b3489d62872c91f9d1f 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlInputToModelTest.java
@@ -5,12 +5,9 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
+import org.apache.log4j.Logger;
+import org.junit.Test;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.modifier.Catalysis;
@@ -25,1393 +22,1323 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-import org.apache.log4j.Logger;
-import org.junit.Test;
-
public class ReactionGpmlInputToModelTest extends WikipathwaysTestFunctions {
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlInputToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ArrowInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void DashedLineInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void DashedArrowInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void NecessaryStimulationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BindingInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_binding_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ConversionInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void StimulationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ModificationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CatalystInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void InhibitionInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CleavageInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CovalentBondInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingLeftInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingRightInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void TranscriptionTranslationInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void GapInteractionInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownInhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void NecessaryStimulationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BindingInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ConversionInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void StimulationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void ModificationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CatalystInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownCatalysis);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void InhibitionInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof UnknownInhibition);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CleavageInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void CovalentBondInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingLeftInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void BranchingRightInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void TranscriptionTranslationInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
- @Test
- public void GapInteractionDashedInputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap_input.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNull(product);
- assertNotNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlInputToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ArrowInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedLineInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedArrowInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_binding_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownInhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownCatalysis);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof UnknownInhibition);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionDashedInputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap_input.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNull(product);
+ assertNotNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
index 5e111c94e9bae7235ff377952c974539d67a646c..b9b708663ed00e5489f8461f568fe016c8eeac1a 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlOutputToModelTest.java
@@ -5,12 +5,9 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
+import org.apache.log4j.Logger;
+import org.junit.Test;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.modifier.Catalysis;
@@ -23,1422 +20,1323 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-import org.apache.log4j.Logger;
-import org.junit.Test;
+public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions {
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlOutputToModelTest.class);
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void LineInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ArrowInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedLineInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void DashedArrowInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_binding_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(0, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void GapInteractionOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(1, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TBarInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void NecessaryStimulationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BindingInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ConversionInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void StimulationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof PhysicalStimulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void ModificationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CatalystInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Catalysis);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void InhibitionInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Inhibition);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CleavageInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void CovalentBondInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingLeftInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void BranchingRightInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modifier);
+ }
+
+ assertNotNull(reactant);
+ assertNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void TranscriptionTranslationInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_output.gpml";
+
+ Model model1 = new GPMLToModel().getModel(fileName);
+
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
-public class ReactionGpmlOutputToModelTest extends WikipathwaysTestFunctions{
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlOutputToModelTest.class);
+ @Test
+ public void GapInteractionDashedOutputTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap_output.gpml";
- private ModelComparator mc = new ModelComparator(1.0);
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void LineInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ArrowInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedLineInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedArrowInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_binding_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(0, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(1, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TBarInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void NecessaryStimulationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ConversionInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void StimulationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof PhysicalStimulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ModificationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CatalystInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Catalysis);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void InhibitionInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Inhibition);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CleavageInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void CovalentBondInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modifier);
- }
-
- assertNotNull(reactant);
- assertNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void TranscriptionTranslationInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void GapInteractionDashedOutputTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap_output.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- Product product = null;
- if (reaction.getProducts().size() > 1) {
- product = reaction.getProducts().get(1);
- }
- Reactant reactant = null;
- if (reaction.getReactants().size() > 1) {
- reactant = reaction.getReactants().get(1);
- }
- Modifier modifier = null;
- if (reaction.getModifiers().size() > 0) {
- modifier = reaction.getModifiers().get(0);
- assertTrue(modifier instanceof Modulation);
- }
-
- assertNull(reactant);
- assertNotNull(product);
- assertNull(modifier);
-
- assertEquals(2, getWarnings().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, model1.getReactions().size());
+
+ Reaction reaction = model1.getReactions().iterator().next();
+
+ Product product = null;
+ if (reaction.getProducts().size() > 1) {
+ product = reaction.getProducts().get(1);
+ }
+ Reactant reactant = null;
+ if (reaction.getReactants().size() > 1) {
+ reactant = reaction.getReactants().get(1);
+ }
+ Modifier modifier = null;
+ if (reaction.getModifiers().size() > 0) {
+ modifier = reaction.getModifiers().get(0);
+ assertTrue(modifier instanceof Modulation);
+ }
+
+ assertNull(reactant);
+ assertNotNull(product);
+ assertNull(modifier);
+
+ assertEquals(2, getWarnings().size());
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals(0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
index d2e625d7934f70c4cde11533a3c80ea09d5cb39e..cf21d37c15c14adbe08436d68ffd18b7b9d44d2b 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/ReactionGpmlToModelTest.java
@@ -4,15 +4,9 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-
import org.apache.log4j.Logger;
import org.junit.Test;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -26,1029 +20,853 @@ import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
import lcsb.mapviewer.wikipathway.XML.GPMLToModel;
-public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions{
- /**
- * Default class logger.
- */
- static Logger logger = Logger.getLogger(ReactionGpmlToModelTest.class);
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void LineInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_line.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void ArrowInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_arrow.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof StateTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedArrowInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_arrow.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void DashedLineInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_line.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionTest() throws Exception {
- try {
- // invalid mim_binding (contains only one reactant)
- String fileName = "testFiles/reactions/interaction_mim_binding.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertFalse(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BindingInteractionTest2() throws Exception {
- try {
- // proper mim_binding (contains two reactants)
- String fileName = "testFiles/reactions/interaction_mim_binding2.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(getWarnings().toString(), 0, getWarnings().size());
- assertTrue(reaction instanceof HeterodimerAssociationReaction);
- assertFalse(reaction.isReversible());
- assertEquals(2, reaction.getReactants().size());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingLeftInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_left.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
-
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void BranchingRightInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_branching_right.gpml";
-
- Model model1 = new GPMLToModel().getModel(fileName);
-
- assertEquals(1, model1.getReactions().size());
-
- Reaction reaction = model1.getReactions().iterator().next();
-
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+public class ReactionGpmlToModelTest extends WikipathwaysTestFunctions {
+ /**
+ * Default class logger.
+ */
+ static Logger logger = Logger.getLogger(ReactionGpmlToModelTest.class);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ private ModelComparator mc = new ModelComparator(1.0);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ @Test
+ public void LineInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_line.gpml";
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, model1.getReactions().size());
- @Test
- public void CatalystInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_catalyst.gpml";
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- assertEquals(1, model1.getReactions().size());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(0, mc.compare(model1, model2));
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ @Test
+ public void ArrowInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_arrow.gpml";
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Reaction reaction = model1.getReactions().iterator().next();
- @Test
- public void CleavageInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_cleavage.gpml";
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertFalse(reaction.isReversible());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Reaction reaction = model1.getReactions().iterator().next();
+ @Test
+ public void DashedArrowInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_arrow.gpml";
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof StateTransitionReaction);
- assertFalse(reaction.isReversible());
+ Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, model1.getReactions().size());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- @Test
- public void ConversionInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_conversion.gpml";
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void DashedLineInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_line.gpml";
- assertEquals(1, model1.getReactions().size());
+ Model model1 = new GPMLToModel().getModel(fileName);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof StateTransitionReaction);
- assertFalse(reaction.isReversible());
+ Reaction reaction = model1.getReactions().iterator().next();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void BindingInteractionTest() throws Exception {
+ try {
+ // invalid mim_binding (contains only one reactant)
+ String fileName = "testFiles/reactions/interaction_mim_binding.gpml";
- @Test
- public void CovalentBondInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_covalent_bond.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, model1.getReactions().size());
- assertEquals(1, model1.getReactions().size());
+ Reaction reaction = model1.getReactions().iterator().next();
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ @Test
+ public void BindingInteractionTest2() throws Exception {
+ try {
+ // proper mim_binding (contains two reactants)
+ String fileName = "testFiles/reactions/interaction_mim_binding2.gpml";
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, model1.getReactions().size());
- @Test
- public void GapInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_gap.gpml";
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(getWarnings().toString(), 0, getWarnings().size());
+ assertTrue(reaction instanceof HeterodimerAssociationReaction);
+ assertFalse(reaction.isReversible());
+ assertEquals(2, reaction.getReactants().size());
- assertEquals(1, model1.getReactions().size());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Reaction reaction = model1.getReactions().iterator().next();
+ @Test
+ public void BranchingLeftInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_left.gpml";
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, model1.getReactions().size());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- @Test
- public void InhibitionInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_inhibition.gpml";
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void BranchingRightInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_branching_right.gpml";
- assertEquals(1, model1.getReactions().size());
+ Model model1 = new GPMLToModel().getModel(fileName);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof NegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
+ Reaction reaction = model1.getReactions().iterator().next();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void CatalystInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_catalyst.gpml";
- @Test
- public void ModificationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_modification.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, model1.getReactions().size());
- assertEquals(1, model1.getReactions().size());
+ Reaction reaction = model1.getReactions().iterator().next();
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ @Test
+ public void CleavageInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_cleavage.gpml";
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, model1.getReactions().size());
- @Test
- public void NecessaryStimulationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation.gpml";
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(1, model1.getReactions().size());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
- assertFalse(reaction.isReversible());
+ @Test
+ public void ConversionInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_conversion.gpml";
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Model model1 = new GPMLToModel().getModel(fileName);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(1, model1.getReactions().size());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof StateTransitionReaction);
+ assertFalse(reaction.isReversible());
- @Test
- public void StimulationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_stimulation.gpml";
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(1, model1.getReactions().size());
+ @Test
+ public void CovalentBondInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_covalent_bond.gpml";
- Reaction reaction = model1.getReactions().iterator().next();
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(1, model1.getReactions().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Reaction reaction = model1.getReactions().iterator().next();
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void TranscriptionTranslationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_mim_transcription_translation.gpml";
+ @Test
+ public void GapInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_gap.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ @Test
+ public void InhibitionInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_inhibition.gpml";
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void TbarTranslationInteractionTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_tbar.gpml";
+ assertEquals(1, model1.getReactions().size());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getReactions().size());
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof NegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Reaction reaction = model1.getReactions().iterator().next();
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof NegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ @Test
+ public void ModificationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_modification.gpml";
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Reaction reaction = model1.getReactions().iterator().next();
- @Test
- public void LineAsInteractionTest2() throws Exception {
- try {
- // proper mim_binding (contains two reactants)
- String fileName = "testFiles/reactions/line_as_interaction.gpml";
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Reaction reaction = model1.getReactions().iterator().next();
+ @Test
+ public void NecessaryStimulationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_necessary_stimulation.gpml";
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, model1.getReactions().size());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- @Test
- public void BindingInteractionDashedTest() throws Exception {
- try {
- // invalid mim_binding (contains only one reactant)
- String fileName = "testFiles/reactions/interaction_dashed_mim_binding.gpml";
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void StimulationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_stimulation.gpml";
- assertEquals(1, model1.getReactions().size());
+ Model model1 = new GPMLToModel().getModel(fileName);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ Reaction reaction = model1.getReactions().iterator().next();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof ReducedPhysicalStimulationReaction);
+ assertFalse(reaction.isReversible());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void TranscriptionTranslationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_mim_transcription_translation.gpml";
- @Test
- public void BranchingLeftInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, model1.getReactions().size());
- assertEquals(1, model1.getReactions().size());
+ Reaction reaction = model1.getReactions().iterator().next();
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ @Test
+ public void TbarTranslationInteractionTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_tbar.gpml";
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, model1.getReactions().size());
- @Test
- public void BranchingRightInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right.gpml";
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof NegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(1, model1.getReactions().size());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ @Test
+ public void LineAsInteractionTest2() throws Exception {
+ try {
+ // proper mim_binding (contains two reactants)
+ String fileName = "testFiles/reactions/line_as_interaction.gpml";
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Model model1 = new GPMLToModel().getModel(fileName);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(1, model1.getReactions().size());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- @Test
- public void CatalystInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst.gpml";
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(1, model1.getReactions().size());
+ @Test
+ public void BindingInteractionDashedTest() throws Exception {
+ try {
+ // invalid mim_binding (contains only one reactant)
+ String fileName = "testFiles/reactions/interaction_dashed_mim_binding.gpml";
- Reaction reaction = model1.getReactions().iterator().next();
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(1, model1.getReactions().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Reaction reaction = model1.getReactions().iterator().next();
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void CleavageInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage.gpml";
+ @Test
+ public void BranchingLeftInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_left.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ @Test
+ public void BranchingRightInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_branching_right.gpml";
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void ConversionInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_conversion.gpml";
+ assertEquals(1, model1.getReactions().size());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- Reaction reaction = model1.getReactions().iterator().next();
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ @Test
+ public void CatalystInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_catalyst.gpml";
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Reaction reaction = model1.getReactions().iterator().next();
- @Test
- public void CovalentBondInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond.gpml";
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Reaction reaction = model1.getReactions().iterator().next();
+ @Test
+ public void CleavageInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_cleavage.gpml";
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, model1.getReactions().size());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- @Test
- public void GapInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_gap.gpml";
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void ConversionInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_conversion.gpml";
- assertEquals(1, model1.getReactions().size());
+ Model model1 = new GPMLToModel().getModel(fileName);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, model1.getReactions().size());
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownTransitionReaction);
- assertTrue(reaction.isReversible());
+ Reaction reaction = model1.getReactions().iterator().next();
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Test
+ public void CovalentBondInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_covalent_bond.gpml";
- @Test
- public void InhibitionInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition.gpml";
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, model1.getReactions().size());
- assertEquals(1, model1.getReactions().size());
+ Reaction reaction = model1.getReactions().iterator().next();
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ @Test
+ public void GapInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_gap.gpml";
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, model1.getReactions().size());
- @Test
- public void ModificationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_modification.gpml";
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownTransitionReaction);
+ assertTrue(reaction.isReversible());
- assertEquals(1, model1.getReactions().size());
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Reaction reaction = model1.getReactions().iterator().next();
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(0, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ @Test
+ public void InhibitionInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_inhibition.gpml";
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Model model1 = new GPMLToModel().getModel(fileName);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(1, model1.getReactions().size());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
- @Test
- public void NecessaryStimulationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation.gpml";
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- Model model1 = new GPMLToModel().getModel(fileName);
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- assertEquals(1, model1.getReactions().size());
+ @Test
+ public void ModificationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_modification.gpml";
- Reaction reaction = model1.getReactions().iterator().next();
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(1, model1.getReactions().size());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Reaction reaction = model1.getReactions().iterator().next();
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(0, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- @Test
- public void StimulationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation.gpml";
+ @Test
+ public void NecessaryStimulationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_necessary_stimulation.gpml";
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model1 = new GPMLToModel().getModel(fileName);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, model1.getReactions().size());
- Reaction reaction = model1.getReactions().iterator().next();
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ @Test
+ public void StimulationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_stimulation.gpml";
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model1 = new GPMLToModel().getModel(fileName);
- @Test
- public void TranscriptionTranslationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation.gpml";
+ assertEquals(1, model1.getReactions().size());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Reaction reaction = model1.getReactions().iterator().next();
- assertEquals(1, model1.getReactions().size());
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Reaction reaction = model1.getReactions().iterator().next();
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof PositiveInfluenceReaction);
- assertFalse(reaction.isReversible());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ @Test
+ public void TranscriptionTranslationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_mim_transcription_translation.gpml";
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model model1 = new GPMLToModel().getModel(fileName);
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, model1.getReactions().size());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Reaction reaction = model1.getReactions().iterator().next();
- @Test
- public void TbarTranslationInteractionDashedTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/interaction_dashed_tbar.gpml";
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof PositiveInfluenceReaction);
+ assertFalse(reaction.isReversible());
- Model model1 = new GPMLToModel().getModel(fileName);
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(1, model1.getReactions().size());
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Reaction reaction = model1.getReactions().iterator().next();
+ @Test
+ public void TbarTranslationInteractionDashedTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/interaction_dashed_tbar.gpml";
- assertEquals(1, getWarnings().size());
- assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
- assertFalse(reaction.isReversible());
+ Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(1, model1.getReactions().size());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Reaction reaction = model1.getReactions().iterator().next();
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ assertEquals(1, getWarnings().size());
+ assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
+ assertFalse(reaction.isReversible());
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- @Test
- public void lineLineCombinedReactionsTest() throws Exception {
- try {
- String fileName = "testFiles/reactions/line_line_combined_reaction.gpml";
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
- Model model1 = new GPMLToModel().getModel(fileName);
+ @Test
+ public void lineLineCombinedReactionsTest() throws Exception {
+ try {
+ String fileName = "testFiles/reactions/line_line_combined_reaction.gpml";
- assertEquals(4, model1.getReactions().size());
-
- assertEquals(4, getWarnings().size());
+ Model model1 = new GPMLToModel().getModel(fileName);
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
+ assertEquals(4, model1.getReactions().size());
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ assertEquals(4, getWarnings().size());
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ Model model2 = serializeModelOverCellDesignerParser(model1);
- assertEquals(0, mc.compare(model1, model2));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ assertEquals(0, mc.compare(model1, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
index 25874080f7f2f5d4de3009066ecad3f8ab1a5c0d..fb326be303434c33e6846f6df68b28ad48f6e85e 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.wikipathway;
import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
@@ -13,6 +14,7 @@ import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URL;
import java.net.URLConnection;
+import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.List;
@@ -26,10 +28,6 @@ import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.EventStorageLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-
import org.apache.log4j.Logger;
import org.apache.log4j.spi.LoggingEvent;
import org.junit.After;
@@ -41,194 +39,218 @@ import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+
public abstract class WikipathwaysTestFunctions {
- private Logger logger = Logger.getLogger(WikipathwaysTestFunctions.class);
-
- protected static double EPSILON = Configuration.EPSILON;
-
- private DocumentBuilder db;
-
-
- private EventStorageLoggerAppender appender;
-
- @Before
- public final void _setUp() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- }
-
- @After
- public final void _tearDown() throws Exception {
- Logger.getRootLogger().removeAppender(appender);
- }
-
- protected List<LoggingEvent> getWarnings() {
- return appender.getWarnings();
- }
-
- protected String readFile(String file) throws IOException {
- StringBuilder stringBuilder = new StringBuilder();
- BufferedReader reader = new BufferedReader(new FileReader(file));
- try {
- String line = null;
- String ls = System.getProperty("line.separator");
-
- while ((line = reader.readLine()) != null) {
- stringBuilder.append(line);
- stringBuilder.append(ls);
- }
- } finally {
- reader.close();
- }
-
- return stringBuilder.toString();
- }
-
- protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
- InputSource is = new InputSource();
- is.setCharacterStream(new StringReader(text));
- return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
- }
-
- protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
- File file = new File(fileName);
- InputStream inputStream = new FileInputStream(file);
- Reader reader = null;
- try {
- reader = new InputStreamReader(inputStream, "UTF-8");
- InputSource is = new InputSource(reader);
-
- Document result = getXmlDocumentFromInputSource(is);
- inputStream.close();
- return result;
- } catch (UnsupportedEncodingException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return null;
- }
-
- protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
- DocumentBuilder db;
- try {
- db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
- } catch (ParserConfigurationException e) {
- throw new InvalidXmlSchemaException("Problem with xml parser");
- }
- Document doc = null;
- try {
- doc = db.parse(stream);
- } catch (SAXException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- }
- return doc;
- }
-
- protected String createTmpFileName() {
- try {
- File f = File.createTempFile("prefix", ".txt");
- String filename = f.getName();
- f.delete();
- return filename;
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
-
- protected String nodeToString(Node node) {
- return nodeToString(node, false);
- }
-
- protected String nodeToString(Node node, 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();
- }
-
- protected boolean equalFiles(String fileA, String fileB) throws IOException {
- int BLOCK_SIZE = 65536;
- FileInputStream inputStreamA = new FileInputStream(fileA);
- FileInputStream inputStreamB = new FileInputStream(fileB);
- // vary BLOCK_SIZE to suit yourself.
- // it should probably a factor or multiple of the size of a disk
- // sector/cluster.
- // Note that your max heap size may need to be adjused
- // if you have a very big block size or lots of these comparators.
-
- // assume inputStreamA and inputStreamB are streams from your two files.
- byte[] streamABlock = new byte[BLOCK_SIZE];
- byte[] streamBBlock = new byte[BLOCK_SIZE];
- boolean match = true;
- int bytesReadA = 0;
- int bytesReadB = 0;
- do {
- bytesReadA = inputStreamA.read(streamABlock);
- bytesReadB = inputStreamB.read(streamBBlock);
- match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
- } while (match && (bytesReadA > -1));
- inputStreamA.close();
- inputStreamB.close();
- return match;
- }
-
- public File createTempDirectory() throws IOException {
- final File temp;
-
- temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
-
- if (!(temp.delete())) {
- throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
- }
-
- if (!(temp.mkdir())) {
- throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
- }
-
- return (temp);
- }
-
- protected String getWebpage(String accessUrl) throws IOException {
- String inputLine;
- StringBuilder tmp = new StringBuilder();
- URL url = new URL(accessUrl);
- URLConnection urlConn = url.openConnection();
- BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
-
- while ((inputLine = in.readLine()) != null) {
- tmp.append(inputLine);
- }
- in.close();
- return tmp.toString();
- }
-
- protected Element fileToNode(String filename) throws SAXException, IOException {
- InputStream is = new FileInputStream(new File(filename));
- Document doc = null;
- doc = db.parse(is);
- return doc.getDocumentElement();
- }
-
+ private Logger logger = Logger.getLogger(WikipathwaysTestFunctions.class);
+
+ protected static double EPSILON = Configuration.EPSILON;
+
+ private DocumentBuilder db;
+
+ private EventStorageLoggerAppender appender;
+
+ @Before
+ public final void _setUp() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ }
+
+ @After
+ public final void _tearDown() throws Exception {
+ Logger.getRootLogger().removeAppender(appender);
+ }
+
+ protected List<LoggingEvent> getWarnings() {
+ return appender.getWarnings();
+ }
+
+ protected String readFile(String file) throws IOException {
+ StringBuilder stringBuilder = new StringBuilder();
+ BufferedReader reader = new BufferedReader(new FileReader(file));
+ try {
+ String line = null;
+ String ls = System.getProperty("line.separator");
+
+ while ((line = reader.readLine()) != null) {
+ stringBuilder.append(line);
+ stringBuilder.append(ls);
+ }
+ } finally {
+ reader.close();
+ }
+
+ return stringBuilder.toString();
+ }
+
+ protected Node getNodeFromXmlString(String text) throws InvalidXmlSchemaException {
+ InputSource is = new InputSource();
+ is.setCharacterStream(new StringReader(text));
+ return getXmlDocumentFromInputSource(is).getChildNodes().item(0);
+ }
+
+ protected Document getXmlDocumentFromFile(String fileName) throws InvalidXmlSchemaException, IOException {
+ File file = new File(fileName);
+ InputStream inputStream = new FileInputStream(file);
+ Reader reader = null;
+ try {
+ reader = new InputStreamReader(inputStream, "UTF-8");
+ InputSource is = new InputSource(reader);
+
+ Document result = getXmlDocumentFromInputSource(is);
+ inputStream.close();
+ return result;
+ } catch (UnsupportedEncodingException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ protected Document getXmlDocumentFromInputSource(InputSource stream) throws InvalidXmlSchemaException {
+ DocumentBuilder db;
+ try {
+ db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+ } catch (ParserConfigurationException e) {
+ throw new InvalidXmlSchemaException("Problem with xml parser");
+ }
+ Document doc = null;
+ try {
+ doc = db.parse(stream);
+ } catch (SAXException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ return doc;
+ }
+
+ protected String createTmpFileName() {
+ try {
+ File f = File.createTempFile("prefix", ".txt");
+ String filename = f.getName();
+ f.delete();
+ return filename;
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
+
+ protected String nodeToString(Node node) {
+ return nodeToString(node, false);
+ }
+
+ protected String nodeToString(Node node, 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();
+ }
+
+ protected boolean equalFiles(String fileA, String fileB) throws IOException {
+ int BLOCK_SIZE = 65536;
+ FileInputStream inputStreamA = new FileInputStream(fileA);
+ FileInputStream inputStreamB = new FileInputStream(fileB);
+ // vary BLOCK_SIZE to suit yourself.
+ // it should probably a factor or multiple of the size of a disk
+ // sector/cluster.
+ // Note that your max heap size may need to be adjused
+ // if you have a very big block size or lots of these comparators.
+
+ // assume inputStreamA and inputStreamB are streams from your two files.
+ byte[] streamABlock = new byte[BLOCK_SIZE];
+ byte[] streamBBlock = new byte[BLOCK_SIZE];
+ boolean match = true;
+ int bytesReadA = 0;
+ int bytesReadB = 0;
+ do {
+ bytesReadA = inputStreamA.read(streamABlock);
+ bytesReadB = inputStreamB.read(streamBBlock);
+ match = ((bytesReadA == bytesReadB) && Arrays.equals(streamABlock, streamBBlock));
+ } while (match && (bytesReadA > -1));
+ inputStreamA.close();
+ inputStreamB.close();
+ return match;
+ }
+
+ public File createTempDirectory() throws IOException {
+ final File temp;
+
+ temp = File.createTempFile("temp", Long.toString(System.nanoTime()));
+
+ if (!(temp.delete())) {
+ throw new IOException("Could not delete temp file: " + temp.getAbsolutePath());
+ }
+
+ if (!(temp.mkdir())) {
+ throw new IOException("Could not create temp directory: " + temp.getAbsolutePath());
+ }
+
+ return (temp);
+ }
+
+ protected String getWebpage(String accessUrl) throws IOException {
+ String inputLine;
+ StringBuilder tmp = new StringBuilder();
+ URL url = new URL(accessUrl);
+ URLConnection urlConn = url.openConnection();
+ BufferedReader in = new BufferedReader(new InputStreamReader(urlConn.getInputStream()));
+
+ while ((inputLine = in.readLine()) != null) {
+ tmp.append(inputLine);
+ }
+ in.close();
+ return tmp.toString();
+ }
+
+ protected Element fileToNode(String filename) throws SAXException, IOException {
+ InputStream is = new FileInputStream(new File(filename));
+ Document doc = null;
+ doc = db.parse(is);
+ return doc.getDocumentElement();
+ }
+
+ protected Model serializeModelOverCellDesignerParser(Model model1)
+ throws InconsistentModelException, InvalidInputDataExecption {
+ for (BioEntity bioEntity: model1.getBioEntities()) {
+ bioEntity.setZ(null);
+ }
+ new ZIndexPopulator().populateZIndex(model1);
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.model2String(model1);
+ InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ return model2;
+ }
+
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
index df028cd6edd21317141ddab2687ae613135125d6..81f02a65f9d33c5a2f456d70b3fb65f0cfa0c43b 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/BugTest.java
@@ -2,68 +2,59 @@ package lcsb.mapviewer.wikipathway.XML;
import static org.junit.Assert.assertEquals;
-import java.io.ByteArrayInputStream;
import java.io.FileInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
import org.apache.log4j.Logger;
import org.junit.Test;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.wikipathway.WikipathwaysTestFunctions;
public class BugTest extends WikipathwaysTestFunctions {
- Logger logger = Logger.getLogger(BugTest.class);
-
- @Test
- public void testBug319() throws Exception {
- try {
- String fileName = "testFiles/bugs/error_319.gpml";
- FileInputStream fis = new FileInputStream(fileName);
- new GpmlParser().createGraph(fis);
- assertEquals(1, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private ModelComparator mc = new ModelComparator(1.0);
-
- @Test
- public void testBug328() throws Exception {
- try {
- String filename = "testFiles/bugs/error_328.gpml";
- Model model1 = new GPMLToModel().getModel(filename);
-
- assertEquals(7, getWarnings().size());
-
- int complexes = 0;
- for (Element alias : model1.getElements()) {
- if (alias instanceof Complex) {
- complexes++;
- }
- }
- assertEquals("Invalid number of complexes", 1, complexes);
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.model2String(model1);
- InputStream is = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
-
- Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
-
- assertEquals("File " + filename + " different after transformation", 0, mc.compare(model1, model2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(BugTest.class);
+
+ @Test
+ public void testBug319() throws Exception {
+ try {
+ String fileName = "testFiles/bugs/error_319.gpml";
+ FileInputStream fis = new FileInputStream(fileName);
+ new GpmlParser().createGraph(fis);
+ assertEquals(1, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private ModelComparator mc = new ModelComparator(1.0);
+
+ @Test
+ public void testBug328() throws Exception {
+ try {
+ String filename = "testFiles/bugs/error_328.gpml";
+ Model model1 = new GPMLToModel().getModel(filename);
+
+ assertEquals(7, getWarnings().size());
+
+ int complexes = 0;
+ for (Element alias : model1.getElements()) {
+ if (alias instanceof Complex) {
+ complexes++;
+ }
+ }
+ assertEquals("Invalid number of complexes", 1, complexes);
+
+ Model model2 = serializeModelOverCellDesignerParser(model1);
+
+ assertEquals("File " + filename + " different after transformation", 0, mc.compare(model1, model2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
index a23566e0385db48d0725ec179c8bf0d1709c67cc..555d8b58e33fcb2c7aa15386f3967bc422721edf 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelContructorTest.java
@@ -4,42 +4,88 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.nio.charset.StandardCharsets;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.graphics.PolylineData;
-
+import org.apache.log4j.Logger;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+
public class ModelContructorTest {
+ Logger logger = Logger.getLogger(ModelContructorTest.class);
+
+ ModelComparator comparator = new ModelComparator();
+
+ private int elementCounter = 0;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testSplitPolyline() {
+ try {
+ Point2D p1 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
+ Point2D p2 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
+ PolylineData pd = new PolylineData(p1, p2);
+
+ ModelContructor mc = new ModelContructor();
+ Pair<PolylineData, PolylineData> result = mc.splitPolyline(pd);
+ assertNotNull(result);
+ assertNotNull(result.getLeft());
+ assertNotNull(result.getRight());
+ assertEquals(2, result.getLeft().getPoints().size());
+ assertEquals(2, result.getRight().getPoints().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testZIndexForElement() throws Exception {
+ try {
+ ModelToGPML parser = new ModelToGPML();
+ Model model = createEmptyModel();
+ model.addElement(createProtein());
+ String xml = parser.getGPML(model);
+ assertNotNull(xml);
+
+ Model model2 = new GPMLToModel().getModel(new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8)));
+ assertEquals(0, comparator.compare(model2, model));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createEmptyModel() {
+ Model result = new ModelFullIndexed(null);
+ result.setWidth(640);
+ result.setHeight(480);
+ return result;
+ }
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void test() {
- try {
- Point2D p1 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
- Point2D p2 = new Point2D.Double(1455.5988605049254, 562.0578193221613);
- PolylineData pd = new PolylineData(p1, p2);
-
- ModelContructor mc = new ModelContructor();
- Pair<PolylineData,PolylineData> result = mc.splitPolyline(pd);
- assertNotNull(result);
- assertNotNull(result.getLeft());
- assertNotNull(result.getRight());
- assertEquals(2, result.getLeft().getPoints().size());
- assertEquals(2, result.getRight().getPoints().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ private GenericProtein createProtein() {
+ GenericProtein result = new GenericProtein("s" + (elementCounter++));
+ result.setX(100);
+ result.setY(20);
+ result.setWidth(100);
+ result.setHeight(30);
+ result.setZ(7890);
+ return result;
+ }
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
index 4f58af9d7590935daffd648009f3f9017427131a..da4ba111370fedcd91c056d0009a8f7011807c25 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/XML/ModelToGPMLTest.java
@@ -61,15 +61,10 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
model.setWidth(1000);
model.setHeight(1000);
- GenericProtein alias = new GenericProtein("sa");
- alias.setName("s2");
- alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
- alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
- alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
- alias.setWidth(10);
- alias.setHeight(10);
- alias.setX(1);
- alias.setY(1);
+ GenericProtein alias = createProtein();
+ alias.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+ alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "123"));
+ alias.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
model.addElement(alias);
@@ -91,4 +86,15 @@ public class ModelToGPMLTest extends WikipathwaysTestFunctions {
throw e;
}
}
+
+ private GenericProtein createProtein() {
+ GenericProtein alias = new GenericProtein("sa");
+ alias.setName("s2");
+ alias.setWidth(10);
+ alias.setHeight(10);
+ alias.setX(1);
+ alias.setY(1);
+ alias.setZ(15);
+ return alias;
+ }
}