export transcription and translation reactions

CHANGELOG

@@ -13,6 +13,8 @@ minerva (15.1.0) unstable; urgency=medium
   * Small improvement: process rectangle can be specified in SBML with reaction
     bounding box (#1292)
   * Small improvement: API allows to remove plugin data entry (#1298)
+  * Small improvement: transport/translation/transcription reactions are
+    exported to SBGN PD (#1302)
   * Bug fix: export to image from selected polygon contained all elements
     inside rectangle bounded by the polygon coordinates (#1096)
   * Bug fix: continuous refreshing list of project when uploading/removing

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -102,7 +102,7 @@ public class SbgnmlXmlExporter {
   ColorParser colorParser = new ColorParser();
 
   XmlAnnotationParser xap = new XmlAnnotationParser(new ArrayList<>(), true);
-  
+
   /**
    * Transforms model into SBGN-ML xml.
    * 
@@ -236,7 +236,7 @@ public class SbgnmlXmlExporter {
 
   private org.w3c.dom.Element getAnnotationExtension(Element element) {
     try {
-      String content =xap.dataSetToXmlString(element.getMiriamData(), element.getElementId());
+      String content = xap.dataSetToXmlString(element.getMiriamData(), element.getElementId());
       content = "<annotation>" + content + "</annotation>";
       DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
       dbf.setNamespaceAware(true);
@@ -710,8 +710,8 @@ public class SbgnmlXmlExporter {
   private GlyphClazz getGlyphClazzFromReaction(Reaction reaction) {
     if (reaction instanceof StateTransitionReaction ||
         reaction instanceof TransportReaction ||
-        reaction instanceof StateTransitionReaction 
-        ) {
+        reaction instanceof TranslationReaction ||
+        reaction instanceof TranscriptionReaction) {
       return GlyphClazz.PROCESS;
     }
     if (reaction instanceof HeterodimerAssociationReaction) {

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java

@@ -21,7 +21,7 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.reaction.*;
-import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.reaction.type.*;
 import lcsb.mapviewer.model.map.species.Ion;
 
 @RunWith(Parameterized.class)
@@ -39,6 +39,8 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
   public static Collection<Object[]> data() throws Exception {
     Collection<Object[]> data = new ArrayList<>();
     data.add(createTestEntry(createReaction(TransportReaction.class)));
+    data.add(createTestEntry(createReaction(TranslationReaction.class)));
+    data.add(createTestEntry(createReaction(TranscriptionReaction.class)));
     return data;
   }
 

model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranscriptionReaction.java

@@ -27,6 +27,10 @@ public class TranscriptionReaction extends Reaction implements SimpleReactionInt
   public TranscriptionReaction() {
     super();
   }
+  
+  public TranscriptionReaction(String elementId) {
+    super(elementId);
+  }
 
   /**
    * Constructor that copies data from the parameter given in the argument.

model/src/main/java/lcsb/mapviewer/model/map/reaction/type/TranslationReaction.java

@@ -29,6 +29,10 @@ public class TranslationReaction extends Reaction implements SimpleReactionInter
     super();
   }
 
+  public TranslationReaction(String elementId) {
+    super(elementId);
+  }
+
   /**
    * Constructor that copies data from the parameter given in the argument.
    *