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 4b81f46..8e8b655 100644 (file)
--- a/forester/java/src/org/forester/protein/Protein.java
+++ b/forester/java/src/org/forester/protein/Protein.java
@@ -38,10 +38,10 @@ 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
@@ -71,4 +71,7 @@ public interface Protein {
     public Species getSpecies();
 
     public List<Domain> getDomainsSortedByPosition();
+
+    public String toDomainArchitectureString( final String separator, final double ie_cutoff );
+    
 }
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