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/extension/multi/MultiPackageNamingUtils.java
similarity index 76%
rename from converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/MultiPackageNamingUtils.java
rename to converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/extension/multi/MultiPackageNamingUtils.java
index 7e00c47184b997e5f7ac4d51b54cde5600feeea5..eefbd1bd251c649fafabc6a80326cc19b6060758 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/extension/multi/MultiPackageNamingUtils.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.extension.multi;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
@@ -26,8 +26,6 @@ public final class MultiPackageNamingUtils {
private static Logger logger = Logger.getLogger(MultiPackageNamingUtils.class);
private static final String MINERVA_MODIFICATION_TYPE_PREFIX = "minerva_modification_type_";
- private static final String MINERVA_POSITION_TO_COMPARTMENT_PREFIX = "minerva_position_to_compartment_";
- private static final String MINERVA_STRUCTURAL_STATE_PREFIX = "minerva_structural_state_";
/**
* Returns id of the {@link MultiSpeciesType} for a given minerva class.
@@ -53,28 +51,16 @@ public final class MultiPackageNamingUtils {
return getSpeciesTypeId(element.getClass());
}
- public static final String getStructuralStateFeatureId(Class<?> speciesClass) {
- return MINERVA_STRUCTURAL_STATE_PREFIX + speciesClass.getSimpleName();
+ public static final String getFeatureId(Class<?> speciesClass, BioEntityFeature feature) {
+ return feature.getIdPrefix() + speciesClass.getSimpleName();
}
- public static String getStructuralStateFeatureId(Species element) {
- return getStructuralStateFeatureId(element.getClass());
+ public static String getFeatureId(Species element, BioEntityFeature feature) {
+ return getFeatureId(element.getClass(), feature);
}
- public static boolean isStructuralStateFeatureId(String featureTypeId) {
- return featureTypeId.startsWith(MINERVA_STRUCTURAL_STATE_PREFIX);
- }
-
- public static final String getPositionToCompartmentFeatureId(Class<?> speciesClass) {
- return MINERVA_POSITION_TO_COMPARTMENT_PREFIX + speciesClass.getSimpleName();
- }
-
- public static String getPositionToCompartmentFeatureId(Species element) {
- return getPositionToCompartmentFeatureId(element.getClass());
- }
-
- public static boolean isPositionToCompartmentFeatureId(String featureTypeId) {
- return featureTypeId.startsWith(MINERVA_POSITION_TO_COMPARTMENT_PREFIX);
+ public static boolean isFeatureId(String featureTypeId, BioEntityFeature feature) {
+ return featureTypeId.startsWith(feature.getIdPrefix());
}
public static String getModificationFeatureId(ModificationResidue mr) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
index 3dfc259f4058b9fc87295aaa720a27a69d945947..d2af7f4ee525de798bb11f7831a1f9a5d6c0e3b8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
@@ -23,10 +23,11 @@ import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
import org.sbml.jsbml.ext.multi.SpeciesFeatureValue;
import org.sbml.jsbml.ext.render.LocalStyle;
-import lcsb.mapviewer.converter.model.sbml.MultiPackageNamingUtils;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.extension.multi.BioEntityFeature;
+import lcsb.mapviewer.converter.model.sbml.extension.multi.MultiPackageNamingUtils;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.AntisenseRna;
import lcsb.mapviewer.model.map.species.Complex;
@@ -215,7 +216,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
- SpeciesFeatureType structuralStateFeature = getStructuralStateFeature(element.getClass(), speciesType);
+ SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType,
+ BioEntityFeature.STRUCTURAL_STATE);
PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(structuralState,
structuralStateFeature);
@@ -261,7 +263,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
if (element.getPositionToCompartment() != null) {
positionToCompartmentName = element.getPositionToCompartment().name();
}
- SpeciesFeatureType structuralStateFeature = getPositionToCompartmentFeature(element.getClass(), speciesType);
+ SpeciesFeatureType structuralStateFeature = getFeature(element.getClass(), speciesType,
+ BioEntityFeature.POSITION_TO_COMPARTMENT);
PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(positionToCompartmentName,
structuralStateFeature);
@@ -343,28 +346,17 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return speciesType;
}
- private SpeciesFeatureType getStructuralStateFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
+ private SpeciesFeatureType getFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType,
+ BioEntityFeature bioEntityFeature) {
SpeciesFeatureType feature = speciesType
- .getSpeciesFeatureType(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
+ .getSpeciesFeatureType(MultiPackageNamingUtils.getFeatureId(clazz, bioEntityFeature));
if (feature == null) {
feature = new SpeciesFeatureType();
- feature.setName("Structural state");
- feature.setId(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
- addPosibleValueToFeature(feature, "");
- speciesType.getListOfSpeciesFeatureTypes().add(feature);
- }
- return feature;
- }
-
- private SpeciesFeatureType getPositionToCompartmentFeature(Class<? extends Element> clazz,
- MultiSpeciesType speciesType) {
- SpeciesFeatureType feature = speciesType
- .getSpeciesFeatureType(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
- if (feature == null) {
- feature = new SpeciesFeatureType();
- feature.setName("Position to compartment");
- feature.setId(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
- addPosibleValueToFeature(feature, "undefined");
+ feature.setName(bioEntityFeature.getFeatureName());
+ feature.setId(MultiPackageNamingUtils.getFeatureId(clazz, bioEntityFeature));
+ if (bioEntityFeature.getDefaultValue() != null) {
+ addPosibleValueToFeature(feature, bioEntityFeature.getDefaultValue());
+ }
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
return feature;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
index 1bdf6ff54812ec2cdedad74d3811bf493579f2c8..12566be85fd5b1500cde88370a22d47e182b881d 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java
@@ -27,8 +27,9 @@ import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.sbml.MultiPackageNamingUtils;
import lcsb.mapviewer.converter.model.sbml.SbmlElementParser;
+import lcsb.mapviewer.converter.model.sbml.extension.multi.BioEntityFeature;
+import lcsb.mapviewer.converter.model.sbml.extension.multi.MultiPackageNamingUtils;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Degraded;
@@ -126,43 +127,35 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
SpeciesFeature feature) {
String warnPrefix = new ElementUtils().getElementTag(minervaElement);
String featureTypeString = feature.getSpeciesFeatureType();
- if (MultiPackageNamingUtils.isStructuralStateFeatureId(featureTypeString)) {
- if (featureTypeString.equals(MultiPackageNamingUtils.getStructuralStateFeatureId(minervaElement))) {
- SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
+ if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.STRUCTURAL_STATE)) {
+ SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
- List<String> structuralStates = new ArrayList<>();
- for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
- PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
- .get(featureValue.getValue());
- structuralStates.add(possibleSpeciesFeatureValue.getName());
- }
- if (minervaElement instanceof Protein) {
- ((Protein) minervaElement).setStructuralState(String.join("; ", structuralStates));
- } else if (minervaElement instanceof Complex) {
- ((Complex) minervaElement).setStructuralState(String.join("; ", structuralStates));
- } else {
- logger.warn(warnPrefix + "Structural state not supported");
- }
+ List<String> structuralStates = new ArrayList<>();
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
+ .get(featureValue.getValue());
+ structuralStates.add(possibleSpeciesFeatureValue.getName());
+ }
+ if (minervaElement instanceof Protein) {
+ ((Protein) minervaElement).setStructuralState(String.join("; ", structuralStates));
+ } else if (minervaElement instanceof Complex) {
+ ((Complex) minervaElement).setStructuralState(String.join("; ", structuralStates));
} else {
- logger.warn(warnPrefix + "Invalid structural state for class " + featureTypeString);
+ logger.warn(warnPrefix + "Structural state not supported");
}
- } else if (MultiPackageNamingUtils.isPositionToCompartmentFeatureId(featureTypeString)) {
- if (featureTypeString.equals(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(minervaElement))) {
- SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
+ } else if (MultiPackageNamingUtils.isFeatureId(featureTypeString, BioEntityFeature.POSITION_TO_COMPARTMENT)) {
+ SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
- List<String> positionToCompartments = new ArrayList<>();
- for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
- PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
- .get(featureValue.getValue());
- positionToCompartments.add(possibleSpeciesFeatureValue.getName());
- }
- if (positionToCompartments.size() != 1) {
- logger.warn(warnPrefix + "Position to compartment must exactly one value");
- } else {
- minervaElement.setPositionToCompartment(PositionToCompartment.getByString(positionToCompartments.get(0)));
- }
+ List<String> positionToCompartments = new ArrayList<>();
+ for (SpeciesFeatureValue featureValue : feature.getListOfSpeciesFeatureValues()) {
+ PossibleSpeciesFeatureValue possibleSpeciesFeatureValue = featureType.getListOfPossibleSpeciesFeatureValues()
+ .get(featureValue.getValue());
+ positionToCompartments.add(possibleSpeciesFeatureValue.getName());
+ }
+ if (positionToCompartments.size() != 1) {
+ logger.warn(warnPrefix + "Position to compartment must exactly one value");
} else {
- logger.warn(warnPrefix + "Position to compartment for class " + featureTypeString);
+ minervaElement.setPositionToCompartment(PositionToCompartment.getByString(positionToCompartments.get(0)));
}
} else if (MultiPackageNamingUtils.isModificationFeatureId(featureTypeString)) {
createModificationResidues(minervaElement, speciesType, feature);
@@ -211,8 +204,10 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
mr = new TranscriptionSite();
if (minervaElement instanceof SpeciesWithTranscriptionSite) {
TranscriptionSite transcriptionSite = (TranscriptionSite) mr;
- transcriptionSite.setActive(MultiPackageNamingUtils.getTranscriptionFactorActiveStateFromFeatureTypeName(featureTypeString));
- transcriptionSite.setDirection(MultiPackageNamingUtils.getTranscriptionFactorDirectionStateFromFeatureTypeName(featureTypeString));
+ transcriptionSite.setActive(
+ MultiPackageNamingUtils.getTranscriptionFactorActiveStateFromFeatureTypeName(featureTypeString));
+ transcriptionSite.setDirection(
+ MultiPackageNamingUtils.getTranscriptionFactorDirectionStateFromFeatureTypeName(featureTypeString));
((SpeciesWithTranscriptionSite) minervaElement).addTranscriptionSite(transcriptionSite);
} else {
logger.warn(warnPrefix + "Object class doesn't support " + mr.getClass());