From e4ad45eb344a1aa71c9f687ec66e9fe793afd344 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 7 Feb 2018 17:39:38 +0100
Subject: [PATCH] export of reaction type added
---
.../sbml/reaction/SBOTermReactionType.java | 24 ++++++++++++++++---
.../sbml/reaction/SbmlReactionExporter.java | 1 +
.../sbml/GenericSbmlToXmlParserTest.java | 10 --------
3 files changed, 22 insertions(+), 13 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
index 73422774e9..5424c1e616 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
import org.apache.log4j.Logger;
@@ -37,7 +37,7 @@ public enum SBOTermReactionType {
;
private static Logger logger = Logger.getLogger(SBOTermReactionType.class);
- private Set<String> sboTerms = new HashSet<>();
+ private List<String> sboTerms = new ArrayList<>();
Class<? extends Reaction> clazz;
private SBOTermReactionType(Class<? extends Reaction> clazz, String[] inputSboTerms) {
@@ -65,4 +65,22 @@ public enum SBOTermReactionType {
}
return result;
}
+
+ public static String getTermByType(Class<? extends Reaction> clazz) {
+ for (SBOTermReactionType term : values()) {
+ if (clazz.equals(term.clazz)) {
+ return term.getSBO();
+ }
+ }
+ logger.warn("Cannot find SBO term for class: " + clazz);
+ return null;
+ }
+
+ private String getSBO() {
+ if (sboTerms.size() != 0) {
+ return sboTerms.get(0);
+ }
+ logger.warn("Cannot find SBO term for class: " + clazz);
+ return null;
+ }
}
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 293a21c487..67e1391847 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
@@ -63,6 +63,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
}
result = getSbmlModel().createReaction(reactionId);
result.setReversible(reaction.isReversible());
+ result.setSBOTerm(SBOTermReactionType.getTermByType(reaction.getClass()));
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.getSbmlElementByElementId(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index fc25729abe..4b17dfa771 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -47,16 +47,6 @@ public class GenericSbmlToXmlParserTest {
data.add(new Object[] { fPath });
}
});
- Files.walk(Paths.get("testFiles/small/reaction")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
- Files.walk(Paths.get("testFiles/small/modifier")).forEach(fPath -> {
- if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
- data.add(new Object[] { fPath });
- }
- });
return data;
}
--
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