From fdf3237e7afb8d6c20bb421c17e3c7780e97dfc5 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 2 Jan 2019 12:15:04 +0100
Subject: [PATCH] method to extract id of position to compartment feature
extracted
---
.../model/sbml/MultiPackageNamingUtils.java | 13 +++++++++++++
.../converter/model/sbml/SbmlExporter.java | 15 +++++++--------
.../model/sbml/species/SbmlSpeciesExporter.java | 2 +-
.../model/sbml/species/SbmlSpeciesParser.java | 4 ++--
4 files changed, 23 insertions(+), 11 deletions(-)
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 dc9d228f58..c2905e08ce 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
@@ -14,6 +14,7 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public final class MultiPackageNamingUtils {
+ private static final String MINERVA_POSITION_TO_COMPARTMENT_PREFIX = "minerva_position_to_compartment_";
private static final String MINERVA_STRUCTURAL_STATE_PREFIX = "minerva_structural_state_";
/**
@@ -52,4 +53,16 @@ public final class MultiPackageNamingUtils {
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);
+ }
+
}
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 9021a01c5f..247453556b 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
@@ -37,7 +37,6 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlExporter {
@@ -125,7 +124,7 @@ public class SbmlExporter {
MultiSpeciesType speciesType = speciesTypeByClass.get(species.getClass());
addStructuralStateToPossibleValues(speciesType, species);
if (species instanceof Species) {
- addPositionToCompartmentToPossibleValues(speciesType, ((Species) species).getPositionToCompartment());
+ addPositionToCompartmentToPossibleValues(speciesType, ((Species) species));
}
}
@@ -146,11 +145,11 @@ public class SbmlExporter {
}
- private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, PositionToCompartment position) {
- SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
- .get("minerva_position_to_compartment_" + speciesType.getName());
- if (position != null) {
- addPosibleValueToFeature(feature, position.name());
+ private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, Species species) {
+ if (species.getPositionToCompartment() != null) {
+ SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
+ .get(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(species));
+ addPosibleValueToFeature(feature, species.getPositionToCompartment().name());
}
}
@@ -227,7 +226,7 @@ public class SbmlExporter {
private void createPositionToCompartmentFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
SpeciesFeatureType feature = new SpeciesFeatureType();
feature.setName("Position to compartment");
- feature.setId("minerva_position_to_compartment_" + clazz.getSimpleName());
+ feature.setId(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
addPosibleValueToFeature(feature, "undefined");
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
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 95ad7b4221..dd6773fba2 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
@@ -112,7 +112,7 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
positionToCompartmentName = element.getPositionToCompartment().name();
}
SpeciesFeatureType structuralStateFeature = speciesType
- .getSpeciesFeatureType("minerva_position_to_compartment_" + element.getClass().getSimpleName());
+ .getSpeciesFeatureType(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(element));
PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
for (PossibleSpeciesFeatureValue value : structuralStateFeature.getListOfPossibleSpeciesFeatureValues()) {
if (value.getName().equals(positionToCompartmentName)) {
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 a691c8b681..1c184c1671 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
@@ -126,8 +126,8 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
} else {
logger.warn(warnPrefix + "Invalid structural state for class " + featureTypeString);
}
- } else if (featureTypeString.startsWith("minerva_position_to_compartment_")) {
- if (featureTypeString.equals("minerva_position_to_compartment_" + minervaElement.getClass().getSimpleName())) {
+ } else if (MultiPackageNamingUtils.isPositionToCompartmentFeatureId(featureTypeString)) {
+ if (featureTypeString.equals(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(minervaElement))) {
SpeciesFeatureType featureType = speciesType.getListOfSpeciesFeatureTypes().get(featureTypeString);
List<String> positionToCompartments = new ArrayList<>();
--
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