Support for prefix declarations in OBO format

api/src/main/java/org/semanticweb/owlapi/formats/OBODocumentFormat.java

@@ -21,7 +21,7 @@
  *         Informatics Group
  * @since 2.0.0
  */
-public class OBODocumentFormat extends OWLDocumentFormatImpl {
+public class OBODocumentFormat extends PrefixDocumentFormatImpl {
 
     /**
      * Key for validation parameter. Currently supports Boolean.TRUE and
@@ -36,14 +36,4 @@ public String getKey() {
         return "OBO Format";
     }
 
-    @Override
-    public boolean isPrefixOWLOntologyFormat() {
-        return false;
-    }
-
-    @Override
-    public PrefixDocumentFormat asPrefixOWLOntologyFormat() {
-        throw new UnsupportedOperationException(getClass().getName()
-                + " is not a PrefixDocumentFormat");
-    }
 }

oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java

@@ -253,6 +253,10 @@ public void setObodoc(OBODoc obodoc) {
         this.obodoc = obodoc;
     }
 
+    public Map<String, String> getIdSpaceMap() {
+        return Collections.unmodifiableMap(this.idSpaceMap);
+    }
+
     /**
      * Gets the owl ontology.
      * 
@@ -548,7 +552,12 @@ public void trHeaderFrame(@Nonnull Frame headerFrame) {
                         trAnnotations(clause));
                 }
             } else if (tag == OboFormatTag.TAG_IDSPACE) {
-                // do not translate, as they are just directives? TODO ask Chris
+                for (Clause clause : headerFrame.getClauses(t)) {
+                    Object[] values = clause.getValues().toArray();
+                    String prefix = values[0].toString();
+                    String baseurl = values[1].toString();
+                    idSpaceMap.put(prefix, baseurl);
+                }
             } else if (tag == OboFormatTag.TAG_OWL_AXIOMS) {
                 // in theory, there should only be one tag
                 // but we can silently collapse multiple tags
@@ -1244,6 +1253,12 @@ protected OWLAxiom trGenericClause(@Nonnull OWLAnnotationSubject sub, @Nonnull S
             }
             ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
                 trLiteral(clause.getValue()), annotations);
+        } else if (tagConstant == OboFormatTag.TAG_REPLACED_BY
+                || tagConstant == OboFormatTag.TAG_CONSIDER) {
+            String curie = (String) clause.getValue();
+            IRI iri = oboIdToIRI(curie);
+            ax = fac.getOWLAnnotationAssertionAxiom(trTagToAnnotationProp(tag), sub,
+                 iri, annotations);
         } else {
             // generic
             // System.out.println("generic clause:"+clause);