diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java index 3b691a55b7d4836a72a426b1168cd857cabc0c1f..7e00c47184b997e5f7ac4d51b54cde5600feeea5 100644 --- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java +++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java @@ -18,6 +18,11 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite; * */ public final class MultiPackageNamingUtils { + + /** + * Default logger. + */ + @SuppressWarnings("unused") private static Logger logger = Logger.getLogger(MultiPackageNamingUtils.class); private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_"; diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java index 3e8819a342f1f91c004c230e26bdf9967e09cbb3..79d301288529c66102f0821255a94ecd6b9bda98 100644 --- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java +++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java @@ -3,9 +3,7 @@ package lcsb.mapviewer.converter.model.sbml; import java.io.UnsupportedEncodingException; import java.util.Arrays; import java.util.Collection; -import java.util.HashMap; import java.util.HashSet; -import java.util.Map; import java.util.Set; import javax.xml.stream.XMLStreamException; @@ -19,7 +17,6 @@ import org.sbml.jsbml.ext.layout.Dimensions; import org.sbml.jsbml.ext.layout.Layout; import org.sbml.jsbml.ext.layout.LayoutModelPlugin; import org.sbml.jsbml.ext.multi.MultiModelPlugin; -import org.sbml.jsbml.ext.multi.MultiSpeciesType; import org.sbml.jsbml.ext.render.GlobalRenderInformation; import org.sbml.jsbml.ext.render.RenderLayoutPlugin; @@ -142,15 +139,12 @@ public class SbmlExporter { return layout; } - private Map<Class<?>, MultiSpeciesType> speciesTypeByClass = new HashMap<>(); - protected MultiModelPlugin createSbmlMultiPlugin(Model result) { MultiModelPlugin multiPlugin = new MultiModelPlugin(result); result.addExtension("multi", multiPlugin); return multiPlugin; } - /** * Creates SBML render plugin for SBML model. * diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java index 257a39e6ce645ffac9fa5837eb2476b8d1008a62..1c0323f3267b8ea24b9ec972c8b982de815f2982 100644 --- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java +++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java @@ -17,7 +17,6 @@ import org.sbml.jsbml.Species; import org.sbml.jsbml.SpeciesReference; import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph; import org.sbml.jsbml.ext.layout.Curve; -import org.sbml.jsbml.ext.layout.Layout; import org.sbml.jsbml.ext.layout.LineSegment; import org.sbml.jsbml.ext.layout.Point; import org.sbml.jsbml.ext.layout.ReactionGlyph; @@ -51,10 +50,15 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb /** * Default class logger. */ + @SuppressWarnings("unused") private static Logger logger = Logger.getLogger(SbmlReactionExporter.class); + private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter; + private SbmlBioEntityExporter<Compartment, org.sbml.jsbml.Compartment> compartmentExporter; + private Map<ReactionNode, SimpleSpeciesReference> speciesReferenceByReactionNode = new HashMap<>(); + public SbmlReactionExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel, SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter, Collection<SbmlExtension> sbmlExtensions, @@ -64,8 +68,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb this.compartmentExporter = compartmentExporter; } - Map<ReactionNode, SimpleSpeciesReference> speciesReferenceByReactionNode = new HashMap<>(); - @Override public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException { String reactionId = getReactionId(reaction);