JAL-1191 isolated SequenceOntology (BioJava wrapper) to /ext/so folder

[jalview.git] / src / jalview / ext / so / SequenceOntology.java

diff --git a/src/jalview/io/gff/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
similarity index 98%
rename from src/jalview/io/gff/SequenceOntology.java
rename to src/jalview/ext/so/SequenceOntology.java
index b069eef..af80b7a 100644 (file)
--- a/src/jalview/io/gff/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -1,4 +1,6 @@
-package jalview.io.gff;
+package jalview.ext.so;
+
+import jalview.io.gff.SequenceOntologyI;
 
 import java.io.BufferedInputStream;
 import java.io.BufferedReader;
@@ -26,7 +28,7 @@ import org.biojava.nbio.ontology.utils.Annotation;
  * A wrapper class that parses the Sequence Ontology and exposes useful access
  * methods. This version uses the BioJava parser.
  */
-class SequenceOntology implements SequenceOntologyI
+public class SequenceOntology implements SequenceOntologyI
 {
   /*
    * the parsed Ontology data as modelled by BioJava
@@ -58,7 +60,7 @@ class SequenceOntology implements SequenceOntologyI
    * Package private constructor to enforce use of singleton. Parses and caches
    * the SO OBO data file.
    */
-  SequenceOntology()
+  public SequenceOntology()
   {
     termsFound = new ArrayList<String>();
     termsNotFound = new ArrayList<String>();