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Commit c6cf8c95 authored by Piotr Gawron's avatar Piotr Gawron
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removing unused imports

parent 9b038127
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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!560Resolve "add support for modifications and states in sbml export/import"
...@@ -18,6 +18,11 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite; ...@@ -18,6 +18,11 @@ import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
* *
*/ */
public final class MultiPackageNamingUtils { public final class MultiPackageNamingUtils {
/**
* Default logger.
*/
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(MultiPackageNamingUtils.class); private static Logger logger = Logger.getLogger(MultiPackageNamingUtils.class);
private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_"; private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_";
......
...@@ -3,9 +3,7 @@ package lcsb.mapviewer.converter.model.sbml; ...@@ -3,9 +3,7 @@ package lcsb.mapviewer.converter.model.sbml;
import java.io.UnsupportedEncodingException; import java.io.UnsupportedEncodingException;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collection; import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet; import java.util.HashSet;
import java.util.Map;
import java.util.Set; import java.util.Set;
import javax.xml.stream.XMLStreamException; import javax.xml.stream.XMLStreamException;
...@@ -19,7 +17,6 @@ import org.sbml.jsbml.ext.layout.Dimensions; ...@@ -19,7 +17,6 @@ import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout; import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin; import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin; 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.GlobalRenderInformation;
import org.sbml.jsbml.ext.render.RenderLayoutPlugin; import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
...@@ -142,15 +139,12 @@ public class SbmlExporter { ...@@ -142,15 +139,12 @@ public class SbmlExporter {
return layout; return layout;
} }
private Map<Class<?>, MultiSpeciesType> speciesTypeByClass = new HashMap<>();
protected MultiModelPlugin createSbmlMultiPlugin(Model result) { protected MultiModelPlugin createSbmlMultiPlugin(Model result) {
MultiModelPlugin multiPlugin = new MultiModelPlugin(result); MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
result.addExtension("multi", multiPlugin); result.addExtension("multi", multiPlugin);
return multiPlugin; return multiPlugin;
} }
/** /**
* Creates SBML render plugin for SBML model. * Creates SBML render plugin for SBML model.
* *
......
...@@ -17,7 +17,6 @@ import org.sbml.jsbml.Species; ...@@ -17,7 +17,6 @@ import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference; import org.sbml.jsbml.SpeciesReference;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph; import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Curve; 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.LineSegment;
import org.sbml.jsbml.ext.layout.Point; import org.sbml.jsbml.ext.layout.Point;
import org.sbml.jsbml.ext.layout.ReactionGlyph; import org.sbml.jsbml.ext.layout.ReactionGlyph;
...@@ -51,10 +50,15 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb ...@@ -51,10 +50,15 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
/** /**
* Default class logger. * Default class logger.
*/ */
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(SbmlReactionExporter.class); private static Logger logger = Logger.getLogger(SbmlReactionExporter.class);
private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter; private SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter;
private SbmlBioEntityExporter<Compartment, org.sbml.jsbml.Compartment> compartmentExporter; 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, public SbmlReactionExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter, SbmlBioEntityExporter<lcsb.mapviewer.model.map.species.Species, Species> speciesExporter,
Collection<SbmlExtension> sbmlExtensions, Collection<SbmlExtension> sbmlExtensions,
...@@ -64,8 +68,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb ...@@ -64,8 +68,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
this.compartmentExporter = compartmentExporter; this.compartmentExporter = compartmentExporter;
} }
Map<ReactionNode, SimpleSpeciesReference> speciesReferenceByReactionNode = new HashMap<>();
@Override @Override
public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException { public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
String reactionId = getReactionId(reaction); String reactionId = getReactionId(reaction);
......
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