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Commit 4fbcf273 authored by Piotr Gawron's avatar Piotr Gawron
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parsing of reaction type from SBO term added

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1 merge request!186Resolve "upload of sbml"
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java 0 → 100644
+ 68
− 0
View file @ 4fbcf273
package lcsb.mapviewer.converter.model.sbml.reaction;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
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.TruncationReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
public enum SBOTermReactionType {
STATE_TRANSITION(StateTransitionReaction.class, new String[] { "SBO:0000176" }), //
TRANSCRIPTION(TranscriptionReaction.class, new String[] { "SBO:0000183" }), //
TRANSLATION(TranslationReaction.class, new String[] { "SBO:0000184" }), //
TRANSPORT(TransportReaction.class, new String[] { "SBO:0000185" }), //
KNOWN_TRANSITION_OMITTED(KnownTransitionOmittedReaction.class, new String[] { "SBO:0000205" }), //
UNKNOWN_TRANSITION(UnknownTransitionReaction.class, new String[] { "SBO:0000396" }), //
HETERODIMER_ASSOCIATION(HeterodimerAssociationReaction.class, new String[] { "SBO:0000177" }), //
DISSOCIATION(DissociationReaction.class, new String[] { "SBO:0000180" }), //
TRUNCATION(TruncationReaction.class, new String[] { "SBO:0000178" }), //
POSITIVE_INFLUENCE(PositiveInfluenceReaction.class, new String[] { "SBO:0000171" }), //
UNKNOWN_POSITIVE_INFLUENCE(UnknownPositiveInfluenceReaction.class, new String[] { "SBO:0000170" }), //
NEGATIVE_INFLUENCE(NegativeInfluenceReaction.class, new String[] { "SBO:0000407" }), //
UNKNOWN_NEGATIVE_INFLUENCE(UnknownNegativeInfluenceReaction.class, new String[] { "SBO:0000169" }), //
;
private static Logger logger = Logger.getLogger(SBOTermReactionType.class);
private Set<String> sboTerms = new HashSet<>();
Class<? extends Reaction> clazz;
private SBOTermReactionType(Class<? extends Reaction> clazz, String[] inputSboTerms) {
this.clazz = clazz;
for (String string : inputSboTerms) {
sboTerms.add(string);
}
}
public static Class<? extends Reaction> getTypeSBOTerm(String sboTerm) {
if (sboTerm == null || sboTerm.isEmpty()) {
return StateTransitionReaction.class;
}
Class<? extends Reaction> result = null;
for (SBOTermReactionType term : values()) {
for (String string : term.sboTerms) {
if (string.equalsIgnoreCase(sboTerm)) {
result = term.clazz;
}
}
}
if (result == null) {
logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for modifier");
result = StateTransitionReaction.class;
}
return result;
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+ 9
− 2
View file @ 4fbcf273
......@@ -49,7 +49,6 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
......@@ -277,7 +276,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction, Model sbmlModel) throws InvalidInputDataExecption {
Reaction reaction = new StateTransitionReaction();
Reaction reaction = new Reaction();
assignBioEntityData(sbmlReaction, reaction);
reaction.setIdReaction(sbmlReaction.getId());
reaction.setReversible(sbmlReaction.isReversible());
......@@ -305,6 +304,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
try {
Class<? extends Reaction> reactionClass = SBOTermReactionType.getTypeSBOTerm(sbmlReaction.getSBOTermID());
reaction = reactionClass.getConstructor(Reaction.class).newInstance(reaction);
} catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException
| NoSuchMethodException | SecurityException e) {
throw new InvalidInputDataExecption("Problem with creating reaction", e);
}
return reaction;
}
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java
+ 119
− 0
View file @ 4fbcf273
......@@ -17,6 +17,19 @@ import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.modifier.UnknownCatalysis;
import lcsb.mapviewer.model.map.modifier.UnknownInhibition;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
import lcsb.mapviewer.model.map.reaction.type.KnownTransitionOmittedReaction;
import lcsb.mapviewer.model.map.reaction.type.NegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.PositiveInfluenceReaction;
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.TruncationReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownNegativeInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownPositiveInfluenceReaction;
import lcsb.mapviewer.model.map.reaction.type.UnknownTransitionReaction;
public class SbmlReactionParserTest {
Logger logger = Logger.getLogger(SbmlReactionParserTest.class);
......@@ -54,4 +67,110 @@ public class SbmlReactionParserTest {
assertTrue(reaction.getModifiers().iterator().next() instanceof UnknownInhibition);
}
@Test
public void testParseStateTransition() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/state_transition.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof StateTransitionReaction);
}
@Test
public void testParseTranscription() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/transcription.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof TranscriptionReaction);
}
@Test
public void testParseTranslation() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/translation.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof TranslationReaction);
}
@Test
public void testParseTransport() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/transport.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof TransportReaction);
}
@Test
public void testParseKnownTransitionOmitted() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser
.createModel(new ConverterParams().filename("testFiles/small/reaction/known_transition_omitted.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof KnownTransitionOmittedReaction);
}
@Test
public void testParseUnknownTransition() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_transition.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof UnknownTransitionReaction);
}
@Test
public void testParseHeterodimerAssociation() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser
.createModel(new ConverterParams().filename("testFiles/small/reaction/heterodimer_association.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof HeterodimerAssociationReaction);
}
@Test
public void testParseDissociation() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/dissociation.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof DissociationReaction);
}
@Test
public void testParseTruncation() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/truncation.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof TruncationReaction);
}
@Test
public void testParsePositiveInfluence() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/positive_influence.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof PositiveInfluenceReaction);
}
@Test
public void testParseUnknownPositiveInfluence() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_positive_influence.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof UnknownPositiveInfluenceReaction);
}
@Test
public void testParseNegativeInfluence() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/negative_influence.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof NegativeInfluenceReaction);
}
@Test
public void testParseUnknownNegativeInfluence() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/unknown_negative_influence.xml"));
Reaction reaction = model.getReactions().iterator().next();
assertNotNull(reaction);
assertTrue(reaction instanceof UnknownNegativeInfluenceReaction);
}
}
converter-sbml/testFiles/small/reaction/dissociation.xml 0 → 100644
+ 43
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s3" name="nm3">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000180">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
<speciesReference species="s3" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/heterodimer_association.xml 0 → 100644
+ 43
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s3" name="nm3">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000177">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
<speciesReference species="s3" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/known_transition_omitted.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000205">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/negative_influence.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000407">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/positive_influence.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000171">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/state_transition.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000176">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/transcription.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000183">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/translation.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000184">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/transport.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000185">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/truncation.xml 0 → 100644
+ 43
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s3" name="nm3">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000178">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
<speciesReference species="s3" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/unknown_negative_influence.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000169">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/unknown_positive_influence.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000170">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
converter-sbml/testFiles/small/reaction/unknown_transition.xml 0 → 100644
+ 39
− 0
View file @ 4fbcf273
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
<model id="TestGEN">
<annotation/>
<listOfCompartments>
<compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species compartment="cell" initialConcentration="1" id="s1" name="nm1">
<annotation/>
</species>
<species compartment="cell" initialConcentration="1" id="s2" name="nm2">
<annotation/>
</species>
</listOfSpecies>
<listOfReactions>
<reaction id="re1" sboTerm="SBO:0000396">
<listOfReactants>
<speciesReference species="s1" stoichiometry="1"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="s2" stoichiometry="1"/>
</listOfProducts>
</reaction>
</listOfReactions>
</model>
</sbml>
\ No newline at end of file
model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+ 0
− 5
View file @ 4fbcf273
......@@ -30,8 +30,6 @@ import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.SplitOperator;
import lcsb.mapviewer.model.map.reaction.type.TwoProductReactionInterface;
import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
......@@ -206,9 +204,6 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
}
private void modifyReaction(Reaction reaction) {
if (reaction instanceof TwoReactantReactionInterface || reaction instanceof TwoProductReactionInterface) {
throw new NotImplementedException();
}
for (AbstractNode node : reaction.getOperators()) {
reaction.removeNode(node);
}
......
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