Merge branch 'develop' into features/JAL-3010ontologyFeatureSettings

[jalview.git] / src / jalview / io / gff / SequenceOntologyI.java

diff --git a/src/jalview/io/gff/SequenceOntologyI.java b/src/jalview/io/gff/SequenceOntologyI.java
index 307e1d1..e9b9923 100644 (file)
--- a/src/jalview/io/gff/SequenceOntologyI.java
+++ b/src/jalview/io/gff/SequenceOntologyI.java
@@ -20,9 +20,9 @@
  */
 package jalview.io.gff;
 
-import java.util.List;
+import jalview.datamodel.ontology.OntologyI;
 
-public interface SequenceOntologyI
+public interface SequenceOntologyI extends OntologyI
 {
   /*
    * selected commonly used values for quick reference
@@ -62,28 +62,4 @@ public interface SequenceOntologyI
 
   // SO:0000704
   public static final String GENE = "gene";
-
-  public boolean isA(String childTerm, String parentTerm);
-
-  /**
-   * Returns a sorted list of all valid terms queried for (i.e. terms processed
-   * which were valid in the SO), using the friendly description.
-   * 
-   * This can be used to check that any hard-coded stand-in for the full SO
-   * includes all the terms needed for correct processing.
-   * 
-   * @return
-   */
-  public List<String> termsFound();
-
-  /**
-   * Returns a sorted list of all invalid terms queried for (i.e. terms
-   * processed which were not found in the SO), using the friendly description.
-   * 
-   * This can be used to report any 'non-compliance' in data, and/or to report
-   * valid terms missing from any hard-coded stand-in for the full SO.
-   * 
-   * @return
-   */
-  public List<String> termsNotFound();
 }