X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fprotein%2FProtein.java;h=4b81f46c5e0238decba672dc8439c9597ff38b42;hb=d4d61f9d2969283e821f650d031c169899fb3870;hp=a4512dfd76eb2781cc5618fa55abce06207ccc86;hpb=73c5b11c1a00e539afb246e345ebf3f042dded78;p=jalview.git

diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java
index a4512df..4b81f46 100644
--- a/forester/java/src/org/forester/protein/Protein.java
+++ b/forester/java/src/org/forester/protein/Protein.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.protein;
 
@@ -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();
 
@@ -58,15 +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