X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=084b80e4212dc2f22fa8324b452e472c9bd44977;hb=9e926ac4305fd9dff38b6e079e55b4f50664d544;hp=2abb1f8c5096c7de4e7dcca3510225daba0c8a74;hpb=f3f90b8d541ef383d4f1d4cb3c1947200d6983ed;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 2abb1f8..084b80e 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.
  */
@@ -358,6 +358,8 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   HiddenSequences getHiddenSequences();
 
+  HiddenColumns getHiddenColumns();
+
   /**
    * Compact representation of alignment
    * 
@@ -578,13 +580,6 @@ public interface AlignmentI extends AnnotatedCollectionI
    */
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
-  /**
-   * 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.
-   * 
-   * @param hiddenCols
-   * @return
-   */
-  public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+  public void setHiddenColumns(HiddenColumns cols);
 
 }