in progress

[jalview.git] / forester / java / src / org / forester / protein / Protein.java

diff --git a/forester/java/src/org/forester/protein/Protein.java b/forester/java/src/org/forester/protein/Protein.java
index 7206545..4b81f46 100644 (file)
--- 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();
 
@@ -58,15 +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();
 }
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