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 f918d97a6ec7d4101417ecf270b15031cf090ad2..6a7e6d10c7f48261e4506f369742259314358c0f 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
@@ -31,7 +31,6 @@ import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentCollec
import lcsb.mapviewer.converter.model.celldesigner.function.FunctionCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.reaction.UnknownReactionClassException;
import lcsb.mapviewer.converter.model.celldesigner.species.InternalModelSpeciesData;
import lcsb.mapviewer.converter.model.celldesigner.species.SpeciesCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
@@ -241,29 +240,6 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
}
} catch (InvalidXmlSchemaException e) {
throw new InvalidInputDataExecption(e);
- } catch (UnknownReactionClassException e) {
- String type = e.getReactionType();
- String reactionId = e.getReactionId();
- String newType = null;
- if ("CATALYSIS".equalsIgnoreCase(type)) {
- newType = "positive influence";
- } else if ("INHIBITION".equalsIgnoreCase(type)) {
- newType = "negative influence";
- } else if ("UNKNOWN_CATALYSIS".equalsIgnoreCase(type)) {
- newType = "unknown positive influence";
- } else if ("UNKNOWN_INHIBITION".equalsIgnoreCase(type)) {
- newType = "unknown negative influence";
- } else if ("PHYSICAL_STIMULATION".equalsIgnoreCase(type)) {
- newType = "reduced physical stimulation";
- } else if ("MODULATION".equalsIgnoreCase(type)) {
- newType = "reduced modulation";
- } else if ("TRIGGER".equalsIgnoreCase(type)) {
- newType = "reduced trigger";
- } else {
- throw new InvalidInputDataExecption(e);
- }
- throw new InvalidInputDataExecption("Reaction type \"" + type + "\" is inappropriate for reaction " + reactionId
- + ". Suggested type: " + newType + " in the \"Reduced\" notation of CellDesigner.", e);
} catch (CellDesignerParserException e) {
throw new InvalidInputDataExecption(e);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 8eb79c0076059cd62f50f5822a51629ac09f4478..5262e182d05350894003826dd39e66a988914905 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -475,14 +475,12 @@ public class ReactionFromXml extends XmlParser {
* @param result
* initial data
* @return reaction with a new type
- * @throws UnknownReactionClassException
- * thrown when type is invalid
+ * @throws ReactionParserException
*/
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
ReactionLineData rdl = ReactionLineData.getByCellDesignerString(type);
if (rdl == null) {
- throw new UnknownReactionClassException("Unknown CellDesigner class type: " + type + ".", type,
- result.getIdReaction());
+ throw new ReactionParserException("Unknown CellDesigner class type: " + type + ".", result);
}
return rdl.createReaction(result);
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
index 7c08957570f59ed479fd75cc9463268971f16d0a..6c55012a2060f64dd75f88f229f5851b886d291c 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineData.java
@@ -3,15 +3,18 @@ package lcsb.mapviewer.converter.model.celldesigner.reaction;
import java.util.HashMap;
import java.util.Map;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.BooleanLogicGateReaction;
+import lcsb.mapviewer.model.map.reaction.type.CatalysisReaction;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
+import lcsb.mapviewer.model.map.reaction.type.InhibitionReaction;
import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
+import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
+import lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction;
import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.ReducedModulationReaction;
import lcsb.mapviewer.model.map.reaction.type.ReducedPhysicalStimulationReaction;
@@ -20,7 +23,10 @@ import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.TranscriptionReaction;
import lcsb.mapviewer.model.map.reaction.type.TranslationReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownReducedModulationReaction;
@@ -37,328 +43,370 @@ import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
*/
public enum ReactionLineData {
- /**
- * Information about arrows/lines for {@link BooleanLogicGateReaction} class.
- */
- BOOLEAN_LOGIC_GATE(BooleanLogicGateReaction.class, "BOOLEAN_LOGIC_GATE"),
-
- /**
- * Information about arrows/lines for {@link DissociationReaction} class.
- */
- DISSOCIATION(DissociationReaction.class, "DISSOCIATION"),
-
- /**
- * Information about arrows/lines for {@link HeterodimerAssociationReaction}
- * class.
- */
- HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, "HETERODIMER_ASSOCIATION"),
-
- /**
- * Information about arrows/lines for {@link KnownTransitionOmittedReaction}
- * class.
- */
- KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, "KNOWN_TRANSITION_OMITTED"),
-
- /**
- * Information about arrows/lines for {@link NegativeInfluenceReaction} class.
- */
- NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, "NEGATIVE_INFLUENCE", LineType.SOLID, ArrowType.CROSSBAR, 3),
-
- /**
- * Information about arrows/lines for {@link PositiveInfluenceReaction} class.
- */
- POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, "POSITIVE_INFLUENCE", LineType.SOLID, ArrowType.OPEN),
-
- /**
- * Information about arrows/lines for {@link ReducedModulationReaction} class.
- */
- REDUCED_MODULATION(ReducedModulationReaction.class, "REDUCED_MODULATION", LineType.SOLID, ArrowType.BLANK),
-
- /**
- * Information about arrows/lines for
- * {@link ReducedPhysicalStimulationReaction} class.
- */
- REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, "REDUCED_PHYSICAL_STIMULATION", LineType.SOLID, ArrowType.BLANK),
-
- /**
- * Information about arrows/lines for {@link ReducedTriggerReaction} class.
- */
- REDUCED_TRIGGER(ReducedTriggerReaction.class, "REDUCED_TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link StateTransitionReaction} class.
- */
- STATE_TRANSITION(StateTransitionReaction.class, "STATE_TRANSITION"),
-
- /**
- * Information about arrows/lines for {@link TranscriptionReaction} class.
- */
- TRANSCRIPTION(TranscriptionReaction.class, "TRANSCRIPTION", LineType.DASH_DOT_DOT),
-
- /**
- * Information about arrows/lines for {@link TranslationReaction} class.
- */
- TRANSLATION(TranslationReaction.class, "TRANSLATION", LineType.DASH_DOT),
-
- /**
- * Information about arrows/lines for {@link TransportReaction} class.
- */
- TRANSPORT(TransportReaction.class, "TRANSPORT", LineType.SOLID, ArrowType.FULL_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link TruncationReaction} class.
- */
- TRUNCATION(TruncationReaction.class, "TRUNCATION"),
-
- /**
- * Information about arrows/lines for {@link UnknownNegativeInfluenceReaction}
- * class.
- */
- UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, "UNKNOWN_NEGATIVE_INFLUENCE", LineType.DASHED, ArrowType.CROSSBAR, 3),
-
- /**
- * Information about arrows/lines for {@link UnknownPositiveInfluenceReaction}
- * class.
- */
- UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, "UNKNOWN_POSITIVE_INFLUENCE", LineType.DASHED, ArrowType.OPEN),
-
- /**
- * Information about arrows/lines for {@link UnknownReducedModulationReaction}
- * class.
- */
- UNKNOWN_REDUCED_MODEULATION(UnknownReducedModulationReaction.class, "UNKNOWN_REDUCED_MODULATION", LineType.DASHED, ArrowType.DIAMOND),
-
- /**
- * Information about arrows/lines for
- * {@link UnknownReducedPhysicalStimulationReaction} class.
- */
- UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class, "UNKNOWN_REDUCED_PHYSICAL_STIMULATION", LineType.DASHED, //
- ArrowType.BLANK),
-
- /**
- * Information about arrows/lines for {@link UnknownReducedTriggerReaction}
- * class.
- */
- UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, "UNKNOWN_REDUCED_TRIGGER", LineType.DASHED, ArrowType.BLANK_CROSSBAR),
-
- /**
- * Information about arrows/lines for {@link UnknownTransitionReaction} class.
- */
- UNKNOWN_TRANSITION(UnknownTransitionReaction.class, "UNKNOWN_TRANSITION");
-
- /**
- * {@link Reaction} class for which the data is stored.
- */
- private Class<? extends Reaction> reactionClass;
-
- /**
- * Type of arrow that should be used by products.
- */
- private ArrowType productArrowType;
-
- /**
- * Line types that should be used by the reaction.
- */
- private LineType lineType;
-
- /**
- * How much product line should be trimmed at the end.
- */
- private double productLineTrim;
-
- /**
- * String used by CellDesigner to represent reaction.
- */
- private String cellDesignerString;
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString) {
- this(clazz, cellDesignerString, LineType.SOLID);
-
- }
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- * @param lineType
- * {@link #lineType}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType) {
- this(clazz, cellDesignerString, lineType, ArrowType.FULL);
- }
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- * @param lineType
- * {@link #lineType}
- * @param productArrowType
- * {@link #productArrowType}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType, ArrowType productArrowType) {
- this(clazz, cellDesignerString, lineType, productArrowType, 0.0);
- }
-
- /**
- *
- * @param clazz
- * {@link #reactionClass}
- * @param cellDesignerString
- * {@link #cellDesignerString}
- * @param lineType
- * {@link #lineType}
- * @param productArrowType
- * {@link #productArrowType}
- * @param productLineTrim
- * {@link #productLineTrim}
- */
- ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType, ArrowType productArrowType, double productLineTrim) {
- this.reactionClass = clazz;
- this.lineType = lineType;
- this.productArrowType = productArrowType;
- this.productLineTrim = productLineTrim;
- this.cellDesignerString = cellDesignerString;
- }
-
- /**
- * @return the reactionClass
- * @see #reactionClass
- */
- public Class<? extends Reaction> getReactionClass() {
- return reactionClass;
- }
-
- /**
- * @return the productArrowType
- * @see #productArrowType
- */
- public ArrowType getProductArrowType() {
- return productArrowType;
- }
-
- /**
- * @return the lineType
- * @see #lineType
- */
- public LineType getLineType() {
- return lineType;
- }
-
- /**
- * @return the productLineTrim
- * @see #productLineTrim
- */
- public double getProductLineTrim() {
- return productLineTrim;
- }
-
- /**
- * Map used for reverse lookup between {@link Reaction} types and
- * {@link ReactionLineData}.
- */
- private static Map<Class<? extends Reaction>, ReactionLineData> map = null;
-
- /**
- * Map used for reverse lookup between {@link #cellDesignerString} types and
- * {@link ReactionLineData}.
- */
- private static Map<String, ReactionLineData> cellDesignerMap = null;
-
- /**
- * Method that finds {@link ReactionLineData} or given {@link Reaction} type.
- *
- * @param clazz
- * type for which {@link ReactionLineData} will be returned
- * @return {@link ReactionLineData} or given {@link Reaction} type
- */
- public static ReactionLineData getByReactionType(Class<? extends Reaction> clazz) {
- if (map == null) {
- map = new HashMap<Class<? extends Reaction>, ReactionLineData>();
- for (ReactionLineData rld : values()) {
- map.put(rld.getReactionClass(), rld);
- }
- }
- return map.get(clazz);
- }
-
- /**
- * @return the cellDesignerString
- * @see #cellDesignerString
- */
- public String getCellDesignerString() {
- return cellDesignerString;
- }
-
- /**
- * Returns {@link ReactionLineData} identified by CellDEsigner string that
- * identifies this Reaction type.
- *
- * @param type
- * {@link #cellDesignerString}
- * @return {@link ReactionLineData} identified by CellDEsigner string that
- * identifies this Reaction type
- */
- public static ReactionLineData getByCellDesignerString(String type) {
- if (cellDesignerMap == null) {
- cellDesignerMap = new HashMap<String, ReactionLineData>();
- for (ReactionLineData rld : values()) {
- cellDesignerMap.put(rld.getCellDesignerString(), rld);
- }
- }
- return cellDesignerMap.get(type);
- }
-
- /**
- * Creates instance of {@link Reaction} represented by this enum and copies
- * the data from result parameter.
- *
- * @param result
- * original data
- * @return instance of {@link Reaction} represented by this enum and copies
- * the data from result parameter
- */
- public Reaction createReaction(Reaction result) {
- try {
- return reactionClass.getConstructor(Reaction.class).newInstance(result);
- } catch (Exception e) {
- throw new InvalidArgumentException("[" + this.name() + "] Problem with creation the new instance of Reaction for: " + result + ". ");
- }
- }
-
- /**
- * Returns {@link ReactionLineData} that can be aplpied for lines with given
- * line type and arrow type. If there are more then one possibility, one of
- * them will be returned (nothing is guaranteed).
- *
- * @param lineType
- * type of the line for which are looking for
- * {@link ReactionLineData}
- * @param productArrowType
- * type of the arrow for which are looking for
- * {@link ReactionLineData}
- * @return {@link ReactionLineData} that can be aplpied for lines with given
- * line type and arrow type. If there are more then one possibility,
- * one of them will be returned (nothing is guaranteed)
- */
- public static ReactionLineData getByLineType(LineType lineType, ArrowType productArrowType) {
- for (ReactionLineData rld : values()) {
- if (rld.getLineType().equals(lineType) && rld.getProductArrowType().equals(productArrowType)) {
- return rld;
- }
- }
- return null;
- }
+ /**
+ * Information about arrows/lines for {@link BooleanLogicGateReaction} class.
+ */
+ BOOLEAN_LOGIC_GATE(BooleanLogicGateReaction.class, "BOOLEAN_LOGIC_GATE"),
+
+ /**
+ * Information about arrows/lines for {@link CatalysisReaction} class.
+ */
+ CATALYSIS(CatalysisReaction.class, "CATALYSIS", LineType.SOLID, ArrowType.CIRCLE),
+
+ /**
+ * Information about arrows/lines for {@link DissociationReaction} class.
+ */
+ DISSOCIATION(DissociationReaction.class, "DISSOCIATION"),
+
+ /**
+ * Information about arrows/lines for {@link HeterodimerAssociationReaction}
+ * class.
+ */
+ HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, "HETERODIMER_ASSOCIATION"),
+
+ /**
+ * Information about arrows/lines for {@link InhibitionReaction} class.
+ */
+ INHIBITION(InhibitionReaction.class, "INHIBITION", LineType.SOLID, ArrowType.CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link KnownTransitionOmittedReaction}
+ * class.
+ */
+ KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, "KNOWN_TRANSITION_OMITTED"),
+
+ /**
+ * Information about arrows/lines for {@link ModulationReaction} class.
+ */
+ MODULATION(ModulationReaction.class, "MODULATION", LineType.SOLID, ArrowType.DIAMOND),
+
+ /**
+ * Information about arrows/lines for {@link NegativeInfluenceReaction} class.
+ */
+ NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, "NEGATIVE_INFLUENCE", LineType.SOLID, ArrowType.CROSSBAR, 3),
+
+ /**
+ * Information about arrows/lines for {@link PhysicalStimulationReaction} class.
+ */
+ PHYSICAL_STIMULATION(PhysicalStimulationReaction.class, "PHYSICAL_STIMULATION", LineType.SOLID, ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link PositiveInfluenceReaction} class.
+ */
+ POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, "POSITIVE_INFLUENCE", LineType.SOLID, ArrowType.OPEN),
+
+ /**
+ * Information about arrows/lines for {@link ReducedModulationReaction} class.
+ */
+ REDUCED_MODULATION(ReducedModulationReaction.class, "REDUCED_MODULATION", LineType.SOLID, ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link ReducedPhysicalStimulationReaction}
+ * class.
+ */
+ REDUCED_PHYSICAL_STIMULATION(ReducedPhysicalStimulationReaction.class, "REDUCED_PHYSICAL_STIMULATION", LineType.SOLID,
+ ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link ReducedTriggerReaction} class.
+ */
+ REDUCED_TRIGGER(ReducedTriggerReaction.class, "REDUCED_TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link StateTransitionReaction} class.
+ */
+ STATE_TRANSITION(StateTransitionReaction.class, "STATE_TRANSITION"),
+
+ /**
+ * Information about arrows/lines for {@link TranscriptionReaction} class.
+ */
+ TRANSCRIPTION(TranscriptionReaction.class, "TRANSCRIPTION", LineType.DASH_DOT_DOT),
+
+ /**
+ * Information about arrows/lines for {@link TranslationReaction} class.
+ */
+ TRANSLATION(TranslationReaction.class, "TRANSLATION", LineType.DASH_DOT),
+
+ /**
+ * Information about arrows/lines for {@link TransportReaction} class.
+ */
+ TRANSPORT(TransportReaction.class, "TRANSPORT", LineType.SOLID, ArrowType.FULL_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link TriggerReaction} class.
+ */
+ TRIGGER(TriggerReaction.class, "TRIGGER", LineType.SOLID, ArrowType.BLANK_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link TruncationReaction} class.
+ */
+ TRUNCATION(TruncationReaction.class, "TRUNCATION"),
+
+ /**
+ * Information about arrows/lines for {@link UnknownCatalysisReaction} class.
+ */
+ UNKNOWN_CATALYSIS(UnknownCatalysisReaction.class, "UNKNOWN_CATALYSIS", LineType.DASHED, ArrowType.CIRCLE),
+
+ /**
+ * Information about arrows/lines for {@link UnknownInhibitionReaction} class.
+ */
+ UNKNOWN_INHIBITION(UnknownInhibitionReaction.class, "UNKNOWN_INHIBITION", LineType.DASHED, ArrowType.CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link UnknownNegativeInfluenceReaction}
+ * class.
+ */
+ UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, "UNKNOWN_NEGATIVE_INFLUENCE", LineType.DASHED,
+ ArrowType.CROSSBAR, 3),
+
+ /**
+ * Information about arrows/lines for {@link UnknownPositiveInfluenceReaction}
+ * class.
+ */
+ UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, "UNKNOWN_POSITIVE_INFLUENCE", LineType.DASHED,
+ ArrowType.OPEN),
+
+ /**
+ * Information about arrows/lines for {@link UnknownReducedModulationReaction}
+ * class.
+ */
+ UNKNOWN_REDUCED_MODEULATION(UnknownReducedModulationReaction.class, "UNKNOWN_REDUCED_MODULATION", LineType.DASHED,
+ ArrowType.DIAMOND),
+
+ /**
+ * Information about arrows/lines for
+ * {@link UnknownReducedPhysicalStimulationReaction} class.
+ */
+ UNKNOWN_REDUCED_PHYSICAL_STIMULATION(UnknownReducedPhysicalStimulationReaction.class,
+ "UNKNOWN_REDUCED_PHYSICAL_STIMULATION", LineType.DASHED, //
+ ArrowType.BLANK),
+
+ /**
+ * Information about arrows/lines for {@link UnknownReducedTriggerReaction}
+ * class.
+ */
+ UNKNOWN_REDUCED_TRIGGER(UnknownReducedTriggerReaction.class, "UNKNOWN_REDUCED_TRIGGER", LineType.DASHED,
+ ArrowType.BLANK_CROSSBAR),
+
+ /**
+ * Information about arrows/lines for {@link UnknownTransitionReaction} class.
+ */
+ UNKNOWN_TRANSITION(UnknownTransitionReaction.class, "UNKNOWN_TRANSITION");
+
+ /**
+ * {@link Reaction} class for which the data is stored.
+ */
+ private Class<? extends Reaction> reactionClass;
+
+ /**
+ * Type of arrow that should be used by products.
+ */
+ private ArrowType productArrowType;
+
+ /**
+ * Line types that should be used by the reaction.
+ */
+ private LineType lineType;
+
+ /**
+ * How much product line should be trimmed at the end.
+ */
+ private double productLineTrim;
+
+ /**
+ * String used by CellDesigner to represent reaction.
+ */
+ private String cellDesignerString;
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString) {
+ this(clazz, cellDesignerString, LineType.SOLID);
+
+ }
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ * @param lineType
+ * {@link #lineType}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType) {
+ this(clazz, cellDesignerString, lineType, ArrowType.FULL);
+ }
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ * @param lineType
+ * {@link #lineType}
+ * @param productArrowType
+ * {@link #productArrowType}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType,
+ ArrowType productArrowType) {
+ this(clazz, cellDesignerString, lineType, productArrowType, 0.0);
+ }
+
+ /**
+ *
+ * @param clazz
+ * {@link #reactionClass}
+ * @param cellDesignerString
+ * {@link #cellDesignerString}
+ * @param lineType
+ * {@link #lineType}
+ * @param productArrowType
+ * {@link #productArrowType}
+ * @param productLineTrim
+ * {@link #productLineTrim}
+ */
+ ReactionLineData(Class<? extends Reaction> clazz, String cellDesignerString, LineType lineType,
+ ArrowType productArrowType, double productLineTrim) {
+ this.reactionClass = clazz;
+ this.lineType = lineType;
+ this.productArrowType = productArrowType;
+ this.productLineTrim = productLineTrim;
+ this.cellDesignerString = cellDesignerString;
+ }
+
+ /**
+ * @return the reactionClass
+ * @see #reactionClass
+ */
+ public Class<? extends Reaction> getReactionClass() {
+ return reactionClass;
+ }
+
+ /**
+ * @return the productArrowType
+ * @see #productArrowType
+ */
+ public ArrowType getProductArrowType() {
+ return productArrowType;
+ }
+
+ /**
+ * @return the lineType
+ * @see #lineType
+ */
+ public LineType getLineType() {
+ return lineType;
+ }
+
+ /**
+ * @return the productLineTrim
+ * @see #productLineTrim
+ */
+ public double getProductLineTrim() {
+ return productLineTrim;
+ }
+
+ /**
+ * Map used for reverse lookup between {@link Reaction} types and
+ * {@link ReactionLineData}.
+ */
+ private static Map<Class<? extends Reaction>, ReactionLineData> map = null;
+
+ /**
+ * Map used for reverse lookup between {@link #cellDesignerString} types and
+ * {@link ReactionLineData}.
+ */
+ private static Map<String, ReactionLineData> cellDesignerMap = null;
+
+ /**
+ * Method that finds {@link ReactionLineData} or given {@link Reaction} type.
+ *
+ * @param clazz
+ * type for which {@link ReactionLineData} will be returned
+ * @return {@link ReactionLineData} or given {@link Reaction} type
+ */
+ public static ReactionLineData getByReactionType(Class<? extends Reaction> clazz) {
+ if (map == null) {
+ map = new HashMap<Class<? extends Reaction>, ReactionLineData>();
+ for (ReactionLineData rld : values()) {
+ map.put(rld.getReactionClass(), rld);
+ }
+ }
+ return map.get(clazz);
+ }
+
+ /**
+ * @return the cellDesignerString
+ * @see #cellDesignerString
+ */
+ public String getCellDesignerString() {
+ return cellDesignerString;
+ }
+
+ /**
+ * Returns {@link ReactionLineData} identified by CellDEsigner string that
+ * identifies this Reaction type.
+ *
+ * @param type
+ * {@link #cellDesignerString}
+ * @return {@link ReactionLineData} identified by CellDEsigner string that
+ * identifies this Reaction type
+ */
+ public static ReactionLineData getByCellDesignerString(String type) {
+ if (cellDesignerMap == null) {
+ cellDesignerMap = new HashMap<String, ReactionLineData>();
+ for (ReactionLineData rld : values()) {
+ cellDesignerMap.put(rld.getCellDesignerString(), rld);
+ }
+ }
+ return cellDesignerMap.get(type);
+ }
+
+ /**
+ * Creates instance of {@link Reaction} represented by this enum and copies the
+ * data from result parameter.
+ *
+ * @param result
+ * original data
+ * @return instance of {@link Reaction} represented by this enum and copies the
+ * data from result parameter
+ * @throws ReactionParserException
+ */
+ public Reaction createReaction(Reaction result) throws ReactionParserException {
+ try {
+ return reactionClass.getConstructor(Reaction.class).newInstance(result);
+ } catch (Exception e) {
+ throw new ReactionParserException("Problem with creation the new instance of reaction. ", result, e);
+ }
+ }
+
+ /**
+ * Returns {@link ReactionLineData} that can be aplpied for lines with given
+ * line type and arrow type. If there are more then one possibility, one of them
+ * will be returned (nothing is guaranteed).
+ *
+ * @param lineType
+ * type of the line for which are looking for {@link ReactionLineData}
+ * @param productArrowType
+ * type of the arrow for which are looking for {@link ReactionLineData}
+ * @return {@link ReactionLineData} that can be aplpied for lines with given
+ * line type and arrow type. If there are more then one possibility, one
+ * of them will be returned (nothing is guaranteed)
+ */
+ public static ReactionLineData getByLineType(LineType lineType, ArrowType productArrowType) {
+ for (ReactionLineData rld : values()) {
+ if (rld.getLineType().equals(lineType) && rld.getProductArrowType().equals(productArrowType)) {
+ return rld;
+ }
+ }
+ return null;
+ }
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownReactionClassException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownReactionClassException.java
deleted file mode 100644
index cf114341b600d5eb3519bdcbc66b91415a05d061..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownReactionClassException.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-/**
- * Exception thrown when unknown
- * {@link lcsb.mapviewer.model.map.reaction.Reaction} class found.
- *
- * @author Piotr Gawron
- *
- */
-public class UnknownReactionClassException extends ReactionParserException {
-
- /**
- * Type of reaction that was a reason for this exception.
- */
- private String reactionType;
-
- /**
- * Default constructor.
- *
- * @param message
- * message thrown
- * @param type
- * {@link #reactionType}
- * @param reactionId
- * {@link #reactionId}
- */
- public UnknownReactionClassException(String message, String type, String reactionId) {
- super(message, reactionId);
- this.reactionType = type;
- }
-
- /**
- * @return the reactionType
- * @see #reactionType
- */
- public String getReactionType() {
- return reactionType;
- }
-
- /**
- * @param reactionType
- * the reactionType to set
- * @see #reactionType
- */
- public void setReactionType(String reactionType) {
- this.reactionType = reactionType;
- }
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 7784e993cc4a3335ed7c4aa257b1aab4cdc275d6..bdce5e8a510707ef3d9e4769bdd95167d514d627 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -241,6 +241,25 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testModifierReactionModelToXml() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/catalysis.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ String xmlString = parser.toXml(model);
+
+ InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+ Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+ assertEquals(0, comparator.compare(model, model2));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testAutoMapWidth() {
try {
@@ -332,96 +351,6 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
- @Test
- public void testInvalidCatalysisReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/catalysis_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("CATALYSIS"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
- @Test
- public void testInvalidInhibitionReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/inhibition_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("INHIBITION"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
- @Test
- public void testInvalidModulationReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/modulation_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("MODULATION"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
- @Test
- public void testInvalidPhysicalStimulationReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/physical_stimulation_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("PHYSICAL_STIMULATION"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
- @Test
- public void testInvalidTriggerReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/trigger_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("TRIGGER"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
- @Test
- public void testInvalidUnknownCatalysisReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/unknown_catalysis_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("UNKNOWN_CATALYSIS"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
@Test
public void testInvalidBrokenTypeReaction() {
try {
@@ -437,21 +366,6 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
- @Test
- public void testInvalidUnknownInhibitionReaction() {
- try {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- FileInputStream fis = new FileInputStream("testFiles/invalid/unknown_inhibition_reaction.xml");
- parser.createModel(new ConverterParams().inputStream(fis));
- fail("Exception expected");
- } catch (InvalidInputDataExecption e) {
- assertTrue(e.getMessage().contains("UNKNOWN_INHIBITION"));
- } catch (Exception e) {
- e.printStackTrace();
- fail("Exception occured: " + e.getMessage());
- }
- }
-
@Test
public void testToXmlAfterAnnotating() throws Exception {
try {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
index 5284caf287314aba6947d1f9ee7100cc0f2b44f3..736069c5d08eae9326bb5b1ecf1949d634adf8b5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/AllReactionTests.java
@@ -6,6 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ KineticsXmlParserTest.class, //
+ ModificationReactionTest.class, //
ReactionCollectionXmlParserTest.class, //
ReactionFromXmlTest.class, //
ReactionLineDataTest.class, //
@@ -13,7 +14,6 @@ import org.junit.runners.Suite.SuiteClasses;
ReactionParserTests.class, //
ReactionToXmlTest.class, //
UnknownModifierClassExceptionTest.class, //
- UnknownReactionClassExceptionTest.class,//
})
public class AllReactionTests {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..9e7e4627c495e4b991615f7ca25307fd4337be4f
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ModificationReactionTest.java
@@ -0,0 +1,126 @@
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.FileInputStream;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.type.CatalysisReaction;
+import lcsb.mapviewer.model.map.reaction.type.InhibitionReaction;
+import lcsb.mapviewer.model.map.reaction.type.ModulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.PhysicalStimulationReaction;
+import lcsb.mapviewer.model.map.reaction.type.TriggerReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownCatalysisReaction;
+import lcsb.mapviewer.model.map.reaction.type.UnknownInhibitionReaction;
+
+public class ModificationReactionTest extends CellDesignerTestFunctions {
+ Logger logger = Logger.getLogger(ModificationReactionTest.class);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCatalysisReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/catalysis.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(CatalysisReaction.class, model.getReactionByReactionId("re1").getClass());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testInhibitionReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/inhibition.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(InhibitionReaction.class, model.getReactionByReactionId("re2").getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testModulationReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/modulation.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(ModulationReaction.class, model.getReactionByReactionId("re1").getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testPhysicalStimulationReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/physical_stimulation.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(PhysicalStimulationReaction.class, model.getReactionByReactionId("re1").getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testTriggerReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/trigger.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(TriggerReaction.class, model.getReactionByReactionId("re1").getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownCatalysisReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/unknown_catalysis.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(UnknownCatalysisReaction.class, model.getReactionByReactionId("re1").getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUnknownInhibitionReaction() throws Exception {
+ try {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ FileInputStream fis = new FileInputStream("testFiles/reactions/modification_reaction/unknown_inhibition.xml");
+ Model model = parser.createModel(new ConverterParams().inputStream(fis));
+ assertEquals(UnknownInhibitionReaction.class, model.getReactionByReactionId("re1").getClass());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
index 5828d1ac3e8f4d9199240ab107780d512a745f3e..ddcab87314557c09f422504b3ba3a9c39b5695db 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java
@@ -453,7 +453,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// test situation when createProperTypeReaction returns reaction of
// unknown type
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) {
return result;
}
};
@@ -484,7 +484,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
}
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) {
return new NewReactionType(result);
}
};
@@ -508,7 +508,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// reaction with two many base reactants
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
Reaction r = super.createProperTypeReaction(type, result);
r.addReactant(new Reactant());
return r;
@@ -534,7 +534,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// reaction with two many base products
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
Reaction r = super.createProperTypeReaction(type, result);
r.addProduct(new Product());
return r;
@@ -568,7 +568,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
}
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) {
return new NewReactionType(result);
}
};
@@ -591,7 +591,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// reaction with two many base reactants
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
Reaction r = super.createProperTypeReaction(type, result);
r.addReactant(new Reactant());
return r;
@@ -616,7 +616,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
// reaction with two many base products
ReactionFromXml parser = new ReactionFromXml(null, false) {
- Reaction createProperTypeReaction(String type, Reaction result) throws UnknownReactionClassException {
+ Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
Reaction r = super.createProperTypeReaction(type, result);
r.addProduct(new Product());
return r;
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
index 53643ccffb4009f6ca2fff69098eb5e5ac009533..76bab8805ae98efb943e69b3eeb026ab1b4e4a38 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionLineDataTest.java
@@ -10,47 +10,46 @@ import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.reaction.Reaction;
public class ReactionLineDataTest {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetByLineType() {
- assertNull(ReactionLineData.getByLineType(null, null));
- }
-
- @Test
- public void test() {
- assertNotNull(ReactionLineData.getByCellDesignerString("UNKNOWN_REDUCED_MODULATION"));
- }
-
- @Test
- public void testAllValues() {
- for (ReactionLineData value : ReactionLineData.values()) {
- assertNotNull(ReactionLineData.valueOf(value.toString()));
- }
- }
-
- @Test
- public void testCreateInvalidReaction() {
- try {
- ReactionLineData.TRANSPORT.createReaction(Mockito.mock(Reaction.class));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Problem with creation the new instance of Reaction"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetByLineType() {
+ assertNull(ReactionLineData.getByLineType(null, null));
+ }
+
+ @Test
+ public void test() {
+ assertNotNull(ReactionLineData.getByCellDesignerString("UNKNOWN_REDUCED_MODULATION"));
+ }
+
+ @Test
+ public void testAllValues() {
+ for (ReactionLineData value : ReactionLineData.values()) {
+ assertNotNull(ReactionLineData.valueOf(value.toString()));
+ }
+ }
+
+ @Test
+ public void testCreateInvalidReaction() throws Exception {
+ try {
+ ReactionLineData.TRANSPORT.createReaction(Mockito.mock(Reaction.class));
+ fail("Exception expected");
+ } catch (ReactionParserException e) {
+ assertTrue(e.getMessage().contains("Problem with creation the new instance of reaction"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownReactionClassExceptionTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownReactionClassExceptionTest.java
deleted file mode 100644
index 4ae9c4ef4ebd9f7fdc1712aa65a46f35166dbaac..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/UnknownReactionClassExceptionTest.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.reaction;
-
-import static org.junit.Assert.assertEquals;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class UnknownReactionClassExceptionTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetters() {
- String modificationType = "str";
- UnknownReactionClassException exception = new UnknownReactionClassException(null, null, null);
- exception.setReactionType(modificationType);
- assertEquals(modificationType, exception.getReactionType());
- }
-
-}
diff --git a/converter-CellDesigner/testFiles/invalid/unknown_inhibition_reaction.xml b/converter-CellDesigner/testFiles/invalid/unknown_inhibition_reaction.xml
deleted file mode 100644
index a1108f0624cca6dd27539169c0d9cebf3142f066..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/testFiles/invalid/unknown_inhibition_reaction.xml
+++ /dev/null
@@ -1,153 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
-<model metaid="untitled" id="untitled">
-<annotation>
-<celldesigner:extension>
-<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
-<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
-<celldesigner:listOfCompartmentAliases/>
-<celldesigner:listOfComplexSpeciesAliases/>
-<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="124.0" y="85.0" w="80.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="340.0" y="82.0" w="80.0" h="30.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
-</celldesigner:usualView>
-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-</celldesigner:listOfSpeciesAliases>
-<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins/>
-<celldesigner:listOfGenes/>
-<celldesigner:listOfRNAs/>
-<celldesigner:listOfAntisenseRNAs/>
-<celldesigner:listOfLayers/>
-<celldesigner:listOfBlockDiagrams/>
-</celldesigner:extension>
-</annotation>
-<listOfUnitDefinitions>
-<unitDefinition metaid="substance" id="substance" name="substance">
-<listOfUnits>
-<unit metaid="CDMT00003" kind="mole"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="volume" id="volume" name="volume">
-<listOfUnits>
-<unit metaid="CDMT00004" kind="litre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="area" id="area" name="area">
-<listOfUnits>
-<unit metaid="CDMT00005" kind="metre" exponent="2"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="length" id="length" name="length">
-<listOfUnits>
-<unit metaid="CDMT00006" kind="metre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="time" id="time" name="time">
-<listOfUnits>
-<unit metaid="CDMT00007" kind="second"/>
-</listOfUnits>
-</unitDefinition>
-</listOfUnitDefinitions>
-<listOfCompartments>
-<compartment metaid="default" id="default" size="1" units="volume"/>
-</listOfCompartments>
-<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s4</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-</listOfSpecies>
-<listOfReactions>
-<reaction metaid="re3" id="re3" reversible="false">
-<annotation>
-<celldesigner:extension>
-<celldesigner:reactionType>UNKNOWN_INHIBITION</celldesigner:reactionType>
-<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3"/>
-</celldesigner:baseReactants>
-<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4"/>
-</celldesigner:baseProducts>
-<celldesigner:connectScheme connectPolicy="direct">
-<celldesigner:listOfLineDirection>
-<celldesigner:lineDirection index="0" value="unknown"/>
-</celldesigner:listOfLineDirection>
-</celldesigner:connectScheme>
-<celldesigner:line width="1.0" color="ff000000"/>
-</celldesigner:extension>
-</annotation>
-<listOfReactants>
-<speciesReference metaid="CDMT00008" species="s3">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfReactants>
-<listOfProducts>
-<speciesReference metaid="CDMT00009" species="s4">
-<annotation>
-<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
-</celldesigner:extension>
-</annotation>
-</speciesReference>
-</listOfProducts>
-</reaction>
-</listOfReactions>
-</model>
-</sbml>
diff --git a/converter-CellDesigner/testFiles/invalid/catalysis_reaction.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/catalysis.xml
similarity index 80%
rename from converter-CellDesigner/testFiles/invalid/catalysis_reaction.xml
rename to converter-CellDesigner/testFiles/reactions/modification_reaction/catalysis.xml
index fe0b221fffad29e3917631547e2b4ff4151ea1be..bf4d021f9848b9ab72f05a682f7a2330c5003090 100644
--- a/converter-CellDesigner/testFiles/invalid/catalysis_reaction.xml
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/catalysis.xml
@@ -8,9 +8,9 @@
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="124.0" y="85.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
@@ -27,16 +27,16 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
+<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="340.0" y="82.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
@@ -48,7 +48,9 @@
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
@@ -87,41 +89,41 @@
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
+<celldesigner:name>s1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s4</celldesigner:name>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
-<reaction metaid="re2" id="re2" reversible="false">
+<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>CATALYSIS</celldesigner:reactionType>
<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3">
+<celldesigner:baseReactant species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:baseProduct species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
@@ -134,19 +136,19 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
-<speciesReference metaid="CDMT00001" species="s3">
+<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
+<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
-<speciesReference metaid="CDMT00002" species="s4">
+<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
+<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
diff --git a/converter-CellDesigner/testFiles/reactions/modification_reaction/inhibition.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/inhibition.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f7602639a68ecd67374160c1ab2a4d29c7568c39
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/inhibition.xml
@@ -0,0 +1,159 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re2" id="re2" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>INHIBITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/converter-CellDesigner/testFiles/invalid/modulation_reaction.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/modulation.xml
similarity index 80%
rename from converter-CellDesigner/testFiles/invalid/modulation_reaction.xml
rename to converter-CellDesigner/testFiles/reactions/modification_reaction/modulation.xml
index 29e202c7bd7505fcd676d6dc915c5b73694760b8..bf023f95f2b62feb7c20e00d10d6af8017b873c0 100644
--- a/converter-CellDesigner/testFiles/invalid/modulation_reaction.xml
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/modulation.xml
@@ -8,9 +8,9 @@
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="124.0" y="85.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
@@ -27,16 +27,16 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
+<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="340.0" y="82.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
@@ -48,7 +48,9 @@
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
@@ -87,41 +89,41 @@
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
+<celldesigner:name>s1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s4</celldesigner:name>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
-<reaction metaid="re3" id="re3" reversible="false">
+<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>MODULATION</celldesigner:reactionType>
<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3">
+<celldesigner:baseReactant species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:baseProduct species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
@@ -134,19 +136,19 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
-<speciesReference metaid="CDMT00008" species="s3">
+<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
+<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
-<speciesReference metaid="CDMT00009" species="s4">
+<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
+<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
diff --git a/converter-CellDesigner/testFiles/invalid/physical_stimulation_reaction.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/physical_stimulation.xml
similarity index 80%
rename from converter-CellDesigner/testFiles/invalid/physical_stimulation_reaction.xml
rename to converter-CellDesigner/testFiles/reactions/modification_reaction/physical_stimulation.xml
index afdff5128ae150e9f704beb04d2a64ae0eaa66d5..c993c4f91ddd0e80cd4cbb154acf03434b193b02 100644
--- a/converter-CellDesigner/testFiles/invalid/physical_stimulation_reaction.xml
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/physical_stimulation.xml
@@ -8,9 +8,9 @@
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="124.0" y="85.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
@@ -27,16 +27,16 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
+<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="340.0" y="82.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
@@ -48,7 +48,9 @@
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
@@ -87,41 +89,41 @@
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
+<celldesigner:name>s1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s4</celldesigner:name>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
-<reaction metaid="re3" id="re3" reversible="false">
+<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>PHYSICAL_STIMULATION</celldesigner:reactionType>
<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3">
+<celldesigner:baseReactant species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:baseProduct species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
@@ -134,19 +136,19 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
-<speciesReference metaid="CDMT00008" species="s3">
+<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
+<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
-<speciesReference metaid="CDMT00009" species="s4">
+<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
+<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
diff --git a/converter-CellDesigner/testFiles/invalid/inhibition_reaction.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/trigger.xml
similarity index 79%
rename from converter-CellDesigner/testFiles/invalid/inhibition_reaction.xml
rename to converter-CellDesigner/testFiles/reactions/modification_reaction/trigger.xml
index 4f86186a56af1c19bf33113da713c6896f4481f5..8ba709b833c09f177b05e75b30dee46227343ad1 100644
--- a/converter-CellDesigner/testFiles/invalid/inhibition_reaction.xml
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/trigger.xml
@@ -8,9 +8,9 @@
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="124.0" y="85.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
@@ -27,16 +27,16 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
+<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="340.0" y="82.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
@@ -48,7 +48,9 @@
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
@@ -87,41 +89,41 @@
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
+<celldesigner:name>s1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s4</celldesigner:name>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
-<reaction metaid="re3" id="re3" reversible="false">
+<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
-<celldesigner:reactionType>INHIBITION</celldesigner:reactionType>
+<celldesigner:reactionType>TRIGGER</celldesigner:reactionType>
<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3">
+<celldesigner:baseReactant species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:baseProduct species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
@@ -134,19 +136,19 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
-<speciesReference metaid="CDMT00008" species="s3">
+<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
+<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
-<speciesReference metaid="CDMT00009" species="s4">
+<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
+<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
diff --git a/converter-CellDesigner/testFiles/invalid/unknown_catalysis_reaction.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/unknown_catalysis.xml
similarity index 80%
rename from converter-CellDesigner/testFiles/invalid/unknown_catalysis_reaction.xml
rename to converter-CellDesigner/testFiles/reactions/modification_reaction/unknown_catalysis.xml
index ab49047d48110ea7f179e0a516422baa981acd9c..0c47dc498fa10638f836fb44c614770faf55420d 100644
--- a/converter-CellDesigner/testFiles/invalid/unknown_catalysis_reaction.xml
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/unknown_catalysis.xml
@@ -8,9 +8,9 @@
<celldesigner:listOfCompartmentAliases/>
<celldesigner:listOfComplexSpeciesAliases/>
<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa3" species="s3">
+<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="124.0" y="85.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
@@ -27,16 +27,16 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
-<celldesigner:speciesAlias id="sa4" species="s4">
+<celldesigner:speciesAlias id="sa2" species="s2">
<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="340.0" y="82.0" w="80.0" h="30.0"/>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
</celldesigner:usualView>
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
@@ -48,7 +48,9 @@
</celldesigner:speciesAlias>
</celldesigner:listOfSpeciesAliases>
<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
@@ -87,41 +89,41 @@
<compartment metaid="default" id="default" size="1" units="volume"/>
</listOfCompartments>
<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
+<celldesigner:name>s1</celldesigner:name>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
-<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
-<celldesigner:class>PHENOTYPE</celldesigner:class>
-<celldesigner:name>s4</celldesigner:name>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
-<reaction metaid="re3" id="re3" reversible="false">
+<reaction metaid="re1" id="re1" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>UNKNOWN_CATALYSIS</celldesigner:reactionType>
<celldesigner:baseReactants>
-<celldesigner:baseReactant species="s3" alias="sa3">
+<celldesigner:baseReactant species="s2" alias="sa2">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
-<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:baseProduct species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
@@ -134,19 +136,19 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
-<speciesReference metaid="CDMT00008" species="s3">
+<speciesReference metaid="CDMT00001" species="s2">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa3</celldesigner:alias>
+<celldesigner:alias>sa2</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
-<speciesReference metaid="CDMT00009" species="s4">
+<speciesReference metaid="CDMT00002" species="s1">
<annotation>
<celldesigner:extension>
-<celldesigner:alias>sa4</celldesigner:alias>
+<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
diff --git a/converter-CellDesigner/testFiles/reactions/modification_reaction/unknown_inhibition.xml b/converter-CellDesigner/testFiles/reactions/modification_reaction/unknown_inhibition.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ff2a9e5b4423f723a35eccd055da5994bbce0af2
--- /dev/null
+++ b/converter-CellDesigner/testFiles/reactions/modification_reaction/unknown_inhibition.xml
@@ -0,0 +1,159 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="125.0" y="205.0" w="80.0" h="30.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="30.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffcc99ff" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="139.0" y="48.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>UNKNOWN_INHIBITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..a226aeed7afb929d05c59533673433d4294a27ba
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/CatalysisReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner catalysis reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("CATALYSIS_REACTION")
+public class CatalysisReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public CatalysisReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public CatalysisReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Catalysis";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public CatalysisReaction copy() {
+ if (this.getClass() == CatalysisReaction.class) {
+ return new CatalysisReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..f44a73ee55b9df8afcf7d7dc4938438b42d75c77
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/InhibitionReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner inhibition reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("INHIBITION_REACTION")
+public class InhibitionReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public InhibitionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public InhibitionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Inhibition";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public InhibitionReaction copy() {
+ if (this.getClass() == InhibitionReaction.class) {
+ return new InhibitionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java
new file mode 100644
index 0000000000000000000000000000000000000000..1dcafec54cb8e179a882be3d6af32cd710cacdad
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModifierReactionNotation.java
@@ -0,0 +1,15 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import lcsb.mapviewer.model.map.species.Phenotype;
+
+/**
+ * Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
+ * Reaction} extensions that implements something that should be modifier but is
+ * a reaction to {@link Phenotype}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface ModifierReactionNotation {
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..7c007cf6148705cbac8efaf8e9271bad3fcc1d63
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ModulationReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner modulation reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("MODULATION_REACTION")
+public class ModulationReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public ModulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public ModulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Modulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public ModulationReaction copy() {
+ if (this.getClass() == ModulationReaction.class) {
+ return new ModulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..99a5b46e136ef6d80b7050aa3eb6b52fcace414d
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/PhysicalStimulationReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner physical stimulation reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("PHYSICAL_STIMULATION_REACTION")
+public class PhysicalStimulationReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public PhysicalStimulationReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public PhysicalStimulationReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Physical stimulation";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public PhysicalStimulationReaction copy() {
+ if (this.getClass() == PhysicalStimulationReaction.class) {
+ return new PhysicalStimulationReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
index 56d5895f2f41e027c3be4775177ca0d257d06a08..f0b5da8973baf18f36c3565b28193beb0c800bd9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java
@@ -1,6 +1,7 @@
package lcsb.mapviewer.model.map.reaction.type;
/**
+ *
* Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
* Reaction} extensions that implements reduced notation in CellDesigner. These
* classes should have more than one reactant and product and cannot have any
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..ca7575dde62ab9453b56139eeb20951c2f81a293
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TriggerReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner trigger reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("TRIGGER_REACTION")
+public class TriggerReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public TriggerReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public TriggerReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Trigger";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public TriggerReaction copy() {
+ if (this.getClass() == TriggerReaction.class) {
+ return new TriggerReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..bce08d8bc1e538101d2642192ac789054575c0e5
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownCatalysisReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown catalysis reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_CATALYSIS_REACTION")
+public class UnknownCatalysisReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownCatalysisReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownCatalysisReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown catalysis";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownCatalysisReaction copy() {
+ if (this.getClass() == UnknownCatalysisReaction.class) {
+ return new UnknownCatalysisReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java
new file mode 100644
index 0000000000000000000000000000000000000000..42c4d6ad996d6e7d72bf913f513e1249e5b4dcbf
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/type/UnknownInhibitionReaction.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model.map.reaction.type;
+
+import javax.persistence.DiscriminatorValue;
+import javax.persistence.Entity;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+
+/**
+ * This class defines a standard CellDesigner unknown inhibition reaction.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@DiscriminatorValue("UNKNOWN_INHIBITION_REACTION")
+public class UnknownInhibitionReaction extends Reaction implements SimpleReactionInterface, ModifierReactionNotation {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor.
+ */
+ public UnknownInhibitionReaction() {
+ super();
+ }
+
+ /**
+ * Constructor that copies data from the parameter given in the argument.
+ *
+ * @param result
+ * parent reaction from which we copy data
+ */
+ public UnknownInhibitionReaction(Reaction result) {
+ super(result);
+ if (result.getProducts().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of products must be greater than 0");
+ }
+ if (result.getReactants().size() < 1) {
+ throw new InvalidArgumentException("Reaction cannot be transformed to " + getStringType() + ": number of reactants must be greater than 0");
+ }
+ }
+
+ @Override
+ public String getStringType() {
+ return "Unknown inhibition";
+ }
+
+ @Override
+ public ReactionRect getReactionRect() {
+ return null;
+ }
+
+ @Override
+ public UnknownInhibitionReaction copy() {
+ if (this.getClass() == UnknownInhibitionReaction.class) {
+ return new UnknownInhibitionReaction(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+}