X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=0842d94801128a4a74762077dd7365b82f822cee;hb=6bfaf3d3a82e4eece77dc1c2d83aede7c4dbb690;hp=089a5f68e5491351841bd88eb617f9005caafd53;hpb=951d723ee7a01b954f0af39645e2f1102c1fc99a;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 089a5f6..0842d94 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -18,10 +18,10 @@
  */
 package jalview.datamodel;
 
-import java.awt.*;
-
 import java.util.*;
 
+import java.awt.*;
+
 
 /**
  * DOCUMENT ME!
@@ -111,7 +111,13 @@ public interface SequenceI
      * @return DOCUMENT ME!
      */
     public String getSequence(int start, int end);
-
+    /**
+     * create a new sequence object from start to end of this sequence
+     * @param start int
+     * @param end int
+     * @return SequenceI
+     */
+    public SequenceI getSubSequence(int start, int end);
     /**
      * DOCUMENT ME!
      *
@@ -183,14 +189,6 @@ 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!
@@ -240,9 +238,9 @@ public interface SequenceI
 
     public void setVamsasId(String id);
 
-    public void setDBRef(Vector dbs);
+    public void setDBRef(DBRefEntry[] dbs);
 
-    public Vector getDBRef();
+    public DBRefEntry [] getDBRef();
 
     public void addDBRef(DBRefEntry entry);
 
@@ -256,4 +254,21 @@ public interface SequenceI
 
     public void addAlignmentAnnotation(AlignmentAnnotation annotation);
 
+    public SequenceGroup getHiddenSequences();
+
+    public void addHiddenSequence(SequenceI seq);
+
+    public void showHiddenSequence(SequenceI seq);
+
+    public void changeCase(boolean toUpper, int start, int end);
+
+    public void toggleCase(int start, int end);
+
+  /**
+   * getSubSequence from start to end of sequence
+   * @param start first residue in subSequence
+   * @return SequenceI
+   */
+  public SequenceI getSubSequence(int start);
+
 }