Merge remote-tracking branch 'origin/devel_15.1.x' into merge-15.1.3

CHANGELOG

 minerva (16.0.0~alpha.1) stable; urgency=medium
-  * Backward incompatibilty: deprecated columns in data overlays are no longer
+  * Backward incompatibility: deprecated columns in data overlays are no longer
     supported (#958)
-  * Backward incompatibilty: comment does not contain name anymore (#1070)
-  * Backward incompatibilty: publication pagination API slightly changed (#1007)
-  * Backward incompatibilty: elements in data overlay are returned differently
+  * Backward incompatibility: comment does not contain name anymore (#1070)
+  * Backward incompatibility: publication pagination API slightly changed (#1007)
+  * Backward incompatibility: elements in data overlay are returned differently
     when using data overlay API (#1007)
-  * Improvement: perormance improved - map is available immediatelly after
+  * Improvement: performance improved - map is available immediatelly after
     tomcat starts (#1007)
   * Improvement: minerva does not require huge amounts of memory anymore (#1007)
   * Improvement: data overlay allows for multiple hits per element (#1007)
@@ -17,12 +17,12 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
  -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Feb 2020 08:00:00 +0200
 
 minerva (16.0.0~alpha.0) stable; urgency=medium
-  * Backward incompatibilty: deprecated columns in data overlay table are no
+  * Backward incompatibility: deprecated columns in data overlay table are no
     longer supported: reverseReaction, reaction_identifier, reactionIdentifier,
     reference_genome_type, reference_genome_version, allel_frequency, lineWidth,
     elementIdentifier, references, model_name (#958)
-  * Backward incompatibilty: informationm about old search queries removed from
-    databsae (it can be still accessed using proper log managing)
+  * Backward incompatibility: information about old search queries removed from
+    database (it can be still accessed using proper log managing)
   * Improvement: automatically generated API documentation available in the
     package (#1016)
   * Bug fix: md5 hash function of plugin was not computed properly
@@ -31,6 +31,17 @@ minerva (16.0.0~alpha.0) stable; urgency=medium
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Aug 2020 13:00:00 +0200
 
+minerva (15.1.3) stable; urgency=medium
+  * Bug fix: modifier reactions to phenotype were incorrectly translated to
+    Process Description reactions when exporting to SBGN-ML (#1445)
+  * Bug fix: AND/OR text was missing when drawing diagram as SBGN (#1428)
+  * Bug fix: annotators details changes were not saved in few consecutive
+    updates (#1446)
+  * Bug fix: SearchListener was not triggered when clicking on highlighted
+    elements (#1449)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Tue, 9 Feb 2021 09:00:00 +0200
+
 minerva (15.1.2) stable; urgency=medium
   * Bug fix: automatic annotations are sometimes missing after project upload
    (#1434)
@@ -46,7 +57,7 @@ minerva (15.1.2) stable; urgency=medium
 
 minerva (15.1.1) stable; urgency=medium
   * Bug fix: export to CD maps with species containing ":" or "." in species id
-    generated files that could not be opened in CellDesigner (#1363)
+    generated files that could not be opened in CellDesigner (#1363) 
   * Bug fix: zoom level change was not reflected in the url when submap was
     opened (#1338)
   * Bug fix: API call returning list of overlays returned for non existing

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -152,9 +152,8 @@ public class SbgnmlXmlExporter {
           }
         }
       } catch (Exception ex) {
-        ex.printStackTrace();
         logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction),
-            "Unexpected problem with exporting reaction.");
+            "Unexpected problem with exporting reaction.", ex);
       }
     }
     try {
@@ -742,7 +741,7 @@ public class SbgnmlXmlExporter {
    *          {@link Reaction} to extract {@link GlyphClazz} from
    * @return {@link GlyphClazz} appropriate to given reaction
    */
-  private GlyphClazz getGlyphClazzFromReaction(Reaction reaction) {
+  GlyphClazz getGlyphClazzFromReaction(Reaction reaction) {
     if (reaction instanceof HeterodimerAssociationReaction) {
       return GlyphClazz.ASSOCIATION;
     }
@@ -758,6 +757,9 @@ public class SbgnmlXmlExporter {
     if (reaction instanceof ReducedNotation) {
       return null;
     }
+    if (reaction instanceof ModifierReactionNotation) {
+      return null;
+    }
     return GlyphClazz.PROCESS;
   }
 
@@ -768,7 +770,7 @@ public class SbgnmlXmlExporter {
    *          reduced notation reaction
    * @return arc extracted from given reduced notation reaction
    */
-  private Arc getArcFromReducedReaction(Reaction reaction) {
+  Arc getArcFromReducedReaction(Reaction reaction) {
     if ((reaction.getReactants().size() != 1) || (reaction.getProducts().size() != 1)) {
       logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
           "Reduced notation does not allow to have multiple reactants/products. Reaction skipped");
@@ -777,25 +779,15 @@ public class SbgnmlXmlExporter {
     Arc arc = new Arc();
     arc.setId(reaction.getIdReaction());
 
-    if (reaction instanceof NegativeInfluenceReaction) {
-      arc.setClazz(ArcClazz.INHIBITION.getClazz());
-    } else if (reaction instanceof ReducedModulationReaction) {
-      arc.setClazz(ArcClazz.MODULATION.getClazz());
-    } else if (reaction instanceof ReducedTriggerReaction) {
-      arc.setClazz(ArcClazz.NECESSARY_STIMULATION.getClazz());
-    } else if (reaction instanceof ReducedPhysicalStimulationReaction) {
-      arc.setClazz(ArcClazz.STIMULATION.getClazz());
+    ArcClazz clazz = getArcClassForReducedNotationReaction(reaction);
+    if (clazz != null) {
+      arc.setClazz(clazz.getClazz());
     } else {
       logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction), "Invalid arc type."
           + " Reduced notation reaction found of type that is not compliant with SBGN-ML format.");
       return null;
     }
 
-    if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
-      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction.getProducts().get(0).getElement()),
-          "Found Phenotype being a reactant in process. That is discouraged");
-    }
-
     arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getElement().getElementId()));
     arc.setTarget(sourceTargetMap.get(reaction.getProducts().get(0).getElement().getElementId()));
 
@@ -833,6 +825,45 @@ public class SbgnmlXmlExporter {
     return arc;
   }
 
+  ArcClazz getArcClassForReducedNotationReaction(Reaction reaction) {
+    if (reaction instanceof NegativeInfluenceReaction) {
+      return ArcClazz.INHIBITION;
+    } else if (reaction instanceof ReducedModulationReaction) {
+      return ArcClazz.MODULATION;
+    } else if (reaction instanceof ReducedTriggerReaction) {
+      return ArcClazz.NECESSARY_STIMULATION;
+    } else if (reaction instanceof ReducedPhysicalStimulationReaction) {
+      return ArcClazz.STIMULATION;
+    } else if (reaction instanceof CatalysisReaction) {
+      return ArcClazz.CATALYSIS;
+    } else if (reaction instanceof InhibitionReaction) {
+      return ArcClazz.INHIBITION;
+    } else if (reaction instanceof ModulationReaction) {
+      return ArcClazz.MODULATION;
+    } else if (reaction instanceof PhysicalStimulationReaction) {
+      return ArcClazz.STIMULATION;
+    } else if (reaction instanceof PositiveInfluenceReaction) {
+      return ArcClazz.STIMULATION;
+    } else if (reaction instanceof TriggerReaction) {
+      return ArcClazz.NECESSARY_STIMULATION;
+    } else if (reaction instanceof UnknownCatalysisReaction) {
+      return ArcClazz.CATALYSIS;
+    } else if (reaction instanceof UnknownInhibitionReaction) {
+      return ArcClazz.INHIBITION;
+    } else if (reaction instanceof UnknownNegativeInfluenceReaction) {
+      return ArcClazz.INHIBITION;
+    } else if (reaction instanceof UnknownReducedModulationReaction) {
+      return ArcClazz.MODULATION;
+    } else if (reaction instanceof UnknownReducedPhysicalStimulationReaction) {
+      return ArcClazz.STIMULATION;
+    } else if (reaction instanceof UnknownPositiveInfluenceReaction) {
+      return ArcClazz.STIMULATION;
+    } else if (reaction instanceof UnknownReducedTriggerReaction) {
+      return ArcClazz.NECESSARY_STIMULATION;
+    }
+    return null;
+  }
+
   /**
    * Removes redundant points from the list.
    * 
@@ -954,7 +985,7 @@ public class SbgnmlXmlExporter {
     if (logicArc) {
       arc.setClazz(ArcClazz.LOGIC_ARC.getClazz());
     } else {
-      arc.setClazz(getArcClazzFromNode(node));
+      arc.setClazz(getArcClazzFromNode(node).getClazz());
     }
 
     if (node instanceof Reactant) {
@@ -981,7 +1012,7 @@ public class SbgnmlXmlExporter {
         }
         if (!found) {
           throw new InvalidArgumentException(
-              new ElementUtils().getElementTag((Modifier) node) + "Problem with exportin modifier");
+              new ElementUtils().getElementTag((Modifier) node) + "Problem with exporting modifier");
         }
       }
     } else if (node instanceof NodeOperator) {
@@ -1078,46 +1109,45 @@ public class SbgnmlXmlExporter {
    *          Node to extract {@link ArcClazz} from
    * @return {@link ArcClazz} for given node
    */
-  private String getArcClazzFromNode(AbstractNode node) {
+  private ArcClazz getArcClazzFromNode(AbstractNode node) {
     if (node instanceof Reactant) {
-      return ArcClazz.CONSUMPTION.getClazz();
+      return ArcClazz.CONSUMPTION;
     }
     if (node instanceof Product) {
-      return ArcClazz.PRODUCTION.getClazz();
+      return ArcClazz.PRODUCTION;
     }
     if (node instanceof Catalysis) {
-      return ArcClazz.CATALYSIS.getClazz();
+      return ArcClazz.CATALYSIS;
     }
     if (node instanceof Inhibition) {
-      return ArcClazz.INHIBITION.getClazz();
+      return ArcClazz.INHIBITION;
     }
     if (node instanceof Modulation) {
-      return ArcClazz.MODULATION.getClazz();
+      return ArcClazz.MODULATION;
     }
     if (node instanceof Trigger) {
-      return ArcClazz.NECESSARY_STIMULATION.getClazz();
+      return ArcClazz.NECESSARY_STIMULATION;
     }
     if (node instanceof PhysicalStimulation) {
-      return ArcClazz.STIMULATION.getClazz();
+      return ArcClazz.STIMULATION;
     }
     if (node instanceof NodeOperator) {
       ArrowType arrowType = node.getLine().getEndAtd().getArrowType();
       switch (arrowType) {
       case BLANK:
-        return ArcClazz.STIMULATION.getClazz();
+        return ArcClazz.STIMULATION;
       case BLANK_CROSSBAR:
-        return ArcClazz.NECESSARY_STIMULATION.getClazz();
+        return ArcClazz.NECESSARY_STIMULATION;
       case CIRCLE:
-        return ArcClazz.CATALYSIS.getClazz();
+        return ArcClazz.CATALYSIS;
       case CROSSBAR:
-        return ArcClazz.INHIBITION.getClazz();
+        return ArcClazz.INHIBITION;
       case DIAMOND:
-        return ArcClazz.MODULATION.getClazz();
+        return ArcClazz.MODULATION;
       case NONE:
-        return ArcClazz.LOGIC_ARC.getClazz();
+        return ArcClazz.LOGIC_ARC;
       default:
         throw new InvalidArgumentException();
-
       }
     }
     throw new InvalidArgumentException();

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -605,7 +605,8 @@ public class SbgnmlXmlParser {
           try {
             parsePhenotypeArc(a, model);
           } catch (Exception e) {
-            logger.warn(getTag(a) + "Probelm with exporting arc", e);
+            logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model), "Probelm with importing arc",
+                e);
           }
           break;
         }
@@ -622,12 +623,19 @@ public class SbgnmlXmlParser {
             break;
           }
         }
+        boolean found = false;
         for (Process p : processes) {
           if (p.getCentralPoint().getId().equals(targetGlyph.getId())) {
             p.addInfluenceArc(a);
+            found = true;
             break;
           }
         }
+        if (!found) {
+          logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
+              "Expected PHENOTYPE in reduced notation arc. Arc skipped.");
+        }
+        break;
       } else {
         Port targetPort = (Port) a.getTarget();
         boolean found = false;

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/AllSbgnmlTests.java

@@ -11,6 +11,7 @@ import org.junit.runners.Suite.SuiteClasses;
     ParseNewtExtensionTest.class,
     SbgnmlSerializationTest.class,
     SbgnmlXmlExporterGenericTest.class,
+    SbgnmlXmlExporterGeneric2Test.class,
     SbgnmlXmlExporterTest.class,
     SbgnmlXmlParserTest.class,
     SbgnmlXmlParserTest2.class,

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterGeneric2Test.java

+package lcsb.mapviewer.converter.model.sbgnml;
+
+import static org.junit.Assert.assertEquals;
+
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.common.geometry.PointTransformation;
+import lcsb.mapviewer.converter.*;
+import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
+import lcsb.mapviewer.model.map.species.Ion;
+
+@RunWith(Parameterized.class)
+public class SbgnmlXmlExporterGeneric2Test extends SbgnmlTestFunctions {
+
+  Logger logger = LogManager.getLogger();
+
+  private Model model;
+
+  public SbgnmlXmlExporterGeneric2Test(String name, Model model) {
+    this.model = model;
+  }
+
+  @Parameters(name = "{index} : {0}")
+  public static Collection<Object[]> data() throws Exception {
+    Collection<Object[]> data = new ArrayList<>();
+    data.add(createTestEntry(createReaction(TransportReaction.class)));
+    data.add(createTestEntry(createReaction(TranslationReaction.class)));
+    data.add(createTestEntry(createReaction(TranscriptionReaction.class)));
+    return data;
+  }
+
+  @Test
+  public void test() throws InconsistentModelException, ConverterException, InvalidInputDataExecption {
+    Converter converter = new SbgnmlXmlConverter();
+    String content = converter.model2String(model);
+    assertEquals(0, super.getWarnings().size());
+
+    InputStream is = new ByteArrayInputStream(content.getBytes());
+
+    Model model2 = converter.createModel(new ConverterParams().inputStream(is));
+    assertEquals(1, model2.getReactions().size());
+
+  }
+
+  private static Object[] createTestEntry(Reaction element) {
+    Model result = new ModelFullIndexed(null);
+    result.setIdModel("X");
+    result.setWidth(200);
+    result.setHeight(200);
+    for (ReactionNode node : ((Reaction) element).getReactionNodes()) {
+      result.addElement(node.getElement());
+    }
+    result.addReaction((Reaction) element);
+    return new Object[] { element.getClass().getSimpleName(), result };
+  }
+
+  static int counter = 0;
+
+  private static Reaction createReaction(Class<? extends Reaction> clazz) throws Exception {
+
+    Reaction reaction = clazz.getConstructor(String.class).newInstance(new Object[] { "re" + (counter++) });
+
+    Ion ion = createIon(counter++);
+    Ion ion2 = createIon(counter);
+
+    PointTransformation pt = new PointTransformation();
+
+    Point2D p1 = ion.getCenter();
+    Point2D p4 = ion.getCenter();
+
+    Point2D p2 = pt.getPointOnLine(p1, p4, 0.3);
+    Point2D p3 = pt.getPointOnLine(p1, p4, 0.6);
+
+    reaction.setLine(new PolylineData(p2, p3));
+
+    Reactant reactant = createReactant(ion);
+    reactant.setLine(new PolylineData(p1, p2));
+    reaction.addReactant(reactant);
+
+    Product product = createProduct(ion2);
+    product.setLine(new PolylineData(p3, p4));
+    reaction.addProduct(product);
+
+    return reaction;
+  }
+
+  private static Reactant createReactant(Ion ion) {
+    Reactant result = new Reactant(ion);
+    Point2D point = ion.getCenter();
+    point.setLocation(point.getX() + 300, point.getY());
+    result.setLine(new PolylineData(ion.getCenter(), point));
+    return result;
+  }
+
+  private static Product createProduct(Ion ion) {
+    Product result = new Product(ion);
+    Point2D point = ion.getCenter();
+    point.setLocation(point.getX() + 300, point.getY());
+    result.setLine(new PolylineData(ion.getCenter(), point));
+    return result;
+  }
+
+  private static Ion createIon(int id) {
+    Ion ion = new Ion("x" + id);
+    ion.setName("ion " + id);
+    ion.setWidth(100);
+    ion.setHeight(100);
+    ion.setX(200 * (id % 2 + 1));
+    ion.setY(50 * (id / 2 + 1));
+    ion.setNameBorder(ion.getBorder());
+    ion.setOnlySubstanceUnits(true);
+    ion.setConstant(true);
+    ion.setInitialAmount(2.0);
+    ion.setBoundaryCondition(true);
+    return ion;
+  }
+
+}

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java

 package lcsb.mapviewer.converter.model.sbgnml;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
 
 import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
+import org.sbgn.ArcClazz;
+import org.sbgn.GlyphClazz;
 
 import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.reaction.*;
-import lcsb.mapviewer.model.map.reaction.type.*;
+import lcsb.mapviewer.model.map.reaction.type.ModifierReactionNotation;
+import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
 import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
-@RunWith(Parameterized.class)
 public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
 
   Logger logger = LogManager.getLogger();
 
-  private Model model;
-
-  public SbgnmlXmlExporterTest(String name, Model model) {
-    this.model = model;
-  }
-
-  @Parameters(name = "{index} : {0}")
-  public static Collection<Object[]> data() throws Exception {
-    Collection<Object[]> data = new ArrayList<>();
-    data.add(createTestEntry(createReaction(TransportReaction.class)));
-    data.add(createTestEntry(createReaction(TranslationReaction.class)));
-    data.add(createTestEntry(createReaction(TranscriptionReaction.class)));
-    return data;
-  }
-
   @Test
-  public void test() throws InconsistentModelException, ConverterException {
-    Converter converter = new SbgnmlXmlConverter();
-    converter.model2String(model);
-    assertEquals(0, super.getWarnings().size());
+  public void testGetGlyphClazzFromReaction() throws Exception {
+    ElementUtils eu = new ElementUtils();
+    SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
+    for (Class<? extends Reaction> clazz : eu.getAvailableReactionSubclasses()) {
+      Reaction reaction = createReaction(clazz);
+      GlyphClazz glyph = exporter.getGlyphClazzFromReaction(reaction);
+      if (reaction instanceof ReducedNotation) {
+        assertNull(eu.getElementTag(reaction) + "Reduced notation should be not treated as PROCESS", glyph);
+      } else if (reaction instanceof ModifierReactionNotation) {
+        assertNull(eu.getElementTag(reaction) + "Modifier reactions should be not treated as PROCESS", glyph);
+      } else {
+        assertNotNull(eu.getElementTag(reaction) + "No glyph found", glyph);
+      }
+    }
   }
 
-  private static Object[] createTestEntry(Reaction element) {
-    Model result = new ModelFullIndexed(null);
-    result.setIdModel("X");
-    result.setWidth(200);
-    result.setHeight(200);
-    for (ReactionNode node : ((Reaction) element).getReactionNodes()) {
-      result.addElement(node.getElement());
+  @Test
+  public void testGetArcClassForReducedNotationReaction() throws Exception {
+    ElementUtils eu = new ElementUtils();
+    SbgnmlXmlExporter exporter = new SbgnmlXmlExporter();
+    for (Class<? extends Reaction> clazz : eu.getAvailableReactionSubclasses()) {
+      Reaction reaction = createReaction(clazz);
+      ArcClazz arc = exporter.getArcClassForReducedNotationReaction(reaction);
+      if (reaction instanceof ReducedNotation) {
+        assertNotNull(eu.getElementTag(reaction) + "Reduced notation is not translated properly", arc);
+      } else if (reaction instanceof ModifierReactionNotation) {
+        assertNotNull(eu.getElementTag(reaction) + "Modifier reaction is not translated properly", arc);
+      }
     }
-    result.addReaction((Reaction) element);
-    return new Object[] { element.getClass().getSimpleName(), result };
   }
 
   static int counter = 0;
@@ -71,24 +63,22 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
 
     Ion ion = createIon(counter++);
     Ion ion2 = createIon(counter);
-    
+
     PointTransformation pt = new PointTransformation();
-    
-    
+
     Point2D p1 = ion.getCenter();
     Point2D p4 = ion.getCenter();
-    
+
     Point2D p2 = pt.getPointOnLine(p1, p4, 0.3);
     Point2D p3 = pt.getPointOnLine(p1, p4, 0.6);
-    
-    
+
     reaction.setLine(new PolylineData(p2, p3));
 
     Reactant reactant = createReactant(ion);
     reactant.setLine(new PolylineData(p1, p2));
     reaction.addReactant(reactant);
-    
-    Product product =createProduct(ion2);
+
+    Product product = createProduct(ion2);
     product.setLine(new PolylineData(p3, p4));
     reaction.addProduct(product);
 

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java

@@ -366,7 +366,7 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
    * @param sbgnFormat
    *          true if operator is to be drawn in SBGN format