X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=1f7a232fa5b3e3d6daf6a1b17599943a70186ae0;hb=cb8ec179c020265666678572815ab056a024da22;hp=b7c919782d34612c66cd1ebe14331ae12e433e17;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index b7c9197..1f7a232 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -45,6 +45,7 @@ public interface SequenceI
      */
     public String getName();
 
+
     /**
      * DOCUMENT ME!
      *
@@ -64,7 +65,7 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getDisplayId();
+    public String getDisplayId(boolean jvsuffix);
 
     /**
      * DOCUMENT ME!
@@ -182,14 +183,6 @@ public interface SequenceI
      */
     public void insertCharAt(int i, char c);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     * @param chop DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c, boolean chop);
 
     /**
      * DOCUMENT ME!
@@ -210,26 +203,55 @@ public interface SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public Vector getSequenceFeatures();
+    public SequenceFeature[] getSequenceFeatures();
 
     /**
      * DOCUMENT ME!
      *
      * @param v DOCUMENT ME!
      */
-    public void setSequenceFeatures(Vector v);
+    public void setSequenceFeatures(SequenceFeature [] features);
 
     /**
      * DOCUMENT ME!
      *
      * @param id DOCUMENT ME!
      */
-    public void setPDBId(String id);
+    public void setPDBId(Vector ids);
 
     /**
      * DOCUMENT ME!
      *
      * @return DOCUMENT ME!
      */
-    public String getPDBId();
+    public Vector getPDBId();
+
+    public void addPDBId(PDBEntry entry);
+
+    public String getVamsasId();
+
+    public void setVamsasId(String id);
+
+    public void setDBRef(Vector dbs);
+
+    public Vector getDBRef();
+
+    public void addDBRef(DBRefEntry entry);
+
+    public void addSequenceFeature(SequenceFeature sf);
+
+    public void setDatasetSequence(SequenceI seq);
+
+    public SequenceI getDatasetSequence();
+
+    public AlignmentAnnotation [] getAnnotation();
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation);
+
+    public SequenceGroup getHiddenSequences();
+
+    public void addHiddenSequence(SequenceI seq);
+
+    public void showHiddenSequence(SequenceI seq);
+
 }