X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=db45d1b650e095609fae3307727f2061f7ef8d31;hb=bd6ce8f5f9fc8e5bc8a6188d15987ce0ffd2c1ee;hp=2e61f9d6001a9dd17529baae7d6bbf5ef6a09c94;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2e61f9d..db45d1b 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -5,16 +5,16 @@
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General License 
+ * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General License for more details.
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General License
+ * You should have received a copy of the GNU General Public License
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
@@ -580,15 +580,18 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
+  public void setHiddenColumns(HiddenColumns cols);
+
   /**
-   * Calculate the visible start and end index of an alignment. The result is
-   * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+   * Insert a sequence at a position in an alignment
    * 
-   * @param hiddenCols
-   * @return
+   * @param i
+   *          The idnex of the position.
+   * @param snew
+   *          The new sequence.
    */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+  void insertSequenceAt(int i, SequenceI snew);
 
-  public void setHiddenColumns(HiddenColumns cols);
+  
 
 }