X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fprotein%2FProtein.java;h=4b81f46c5e0238decba672dc8439c9597ff38b42;hb=f4187e1ce2cf7da7e910919f68dd82fea9bccaa2;hp=661636101afa845448ad5d5a3a772048c8bc792e;hpb=ce9e2773527fda17dcd058c8432a3bffbfadecdc;p=jalview.git

diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java
index 6616361..4b81f46 100644
--- a/forester/java/src/org/forester/protein/Protein.java
+++ b/forester/java/src/org/forester/protein/Protein.java
@@ -46,7 +46,7 @@ public interface Protein {
      * @param in_nc_order to consider order
      * @return
      */
-    public boolean contains( final List<DomainId> domains, final boolean in_nc_order );
+    public boolean contains( final List<String> domains, final boolean in_nc_order );
 
     public String getAccession();
 
@@ -58,11 +58,11 @@ public interface Protein {
 
     public Domain getProteinDomain( final int index );
 
-    public int getProteinDomainCount( final DomainId domain_id );
+    public int getProteinDomainCount( final String domain_id );
 
     public List<Domain> getProteinDomains();
 
-    public List<Domain> getProteinDomains( final DomainId domain_id );
+    public List<Domain> getProteinDomains( final String domain_id );
 
     public ProteinId getProteinId();