X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fprotein%2FProtein.java;h=eccc7d7f8b90d15793a8c358a646b943934bb1ed;hb=761719f91261eb049fada546ba363d4693a3bfa7;hp=720654574dcf7fedc004ca226a4f50cc3fb57f52;hpb=656be28debec520e0e35a8b311114398a40ea366;p=jalview.git

diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java
index 7206545..eccc7d7 100644
--- a/forester/java/src/org/forester/protein/Protein.java
+++ b/forester/java/src/org/forester/protein/Protein.java
@@ -38,15 +38,15 @@ public interface Protein {
      * If in_nc_order is set to true, this should return true only and only if
      * the order in List 'domains' and this protein (as determined by the start positions
      * of the domains of this proteins, _not_ by their index) are the same
-     * (interspersing, 'other', domains in this are ignored). 
+     * (interspersing, 'other', domains in this are ignored).
      * If in_nc_order is set to false, this should return true only and only if
      * this contains all domains listed in 'domains' (order and count do not matter).
-     * 
+     *
      * @param domains a list of domain ids in a certain order.
      * @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();
 
@@ -58,15 +58,17 @@ 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();
 
     public int getLength();
 
     public Species getSpecies();
+
+    public List<Domain> getDomainsSortedByPosition();
 }
\ No newline at end of file