X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=2e1daa3976970a15875c47eba74402aba7192e9b;hb=1624d4fc89f17c4a6cdb80b7d4cc37a095b6fe67;hp=2f365e6e113c7c8fc4b4d28082afa7f075f8772c;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 2f365e6..2e1daa3 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,17 +20,16 @@
  */
 package jalview.datamodel;
 
-import jalview.datamodel.Sequence.DBModList;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
 import java.util.BitSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.datamodel.Sequence.DBModList;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
 
 /**
  * Methods for manipulating a sequence, its metadata and related annotation in
@@ -39,7 +38,7 @@ import fr.orsay.lri.varna.models.rna.RNA;
  * @author $author$
  * @version $Revision$
  */
-public interface SequenceI extends ASequenceI
+public interface SequenceI extends ASequenceI, ContactMapHolderI
 {
   /**
    * Set the display name for the sequence
@@ -416,7 +415,7 @@ public interface SequenceI extends ASequenceI
   /**
    * Derive a sequence (using this one's dataset or as the dataset)
    * 
-   * @return duplicate sequence with valid dataset sequence
+   * @return duplicate sequence and any annotation present with valid dataset sequence
    */
   public SequenceI deriveSequence();
 
@@ -597,4 +596,7 @@ public interface SequenceI extends ASequenceI
    */
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm);
+
 }