X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=06e93d7a4322aea1f8b8feb2267d0a071e4f2c22;hb=54904100ca490c7ca4484a88bf40963e48a35eec;hp=19b5b1c25859352069826179e8e5f855e6145ca3;hpb=c16afbb4d0e2672fdc54d32778b6d53f09c5d86c;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 19b5b1c..06e93d7 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -111,17 +111,8 @@ public interface AlignmentI
      * @param start Start index of columns to delete.
      * @param end End index to columns to delete.
      */
-    public void deleteColumns(int start, int end);
+    public void deleteColumns(SequenceI seqs [], int start, int end);
 
-    /**
-     * Deletes all residues in every sequence of alignment within given columns.
-     *
-     * @param seq1 Index of first sequence to delete columns from.
-     * @param seq2 Index of last sequence to delete columns from.
-     * @param start Start index of columns to delete.
-     * @param end End index of columns to delete.
-     */
-    public void deleteColumns(int seq1, int seq2, int start, int end);
 
     /**
      * Finds sequence in alignment using sequence name as query.
@@ -162,15 +153,6 @@ public interface AlignmentI
     public void removeGaps();
 
 
-    /**
-     * Finds group that sequence at index i in alignment is part of.
-     *
-     * @param i Index in alignment.
-     *
-     * @return First group found for sequence at position i. WARNING :
-     * Sequences may be members of several groups. This method is incomplete.
-     */
-    public SequenceGroup findGroup(int i);
 
     /**
      * Finds group that given sequence is part of.
@@ -288,5 +270,9 @@ public interface AlignmentI
     public void adjustSequenceAnnotations();
 
     public HiddenSequences getHiddenSequences();
-
+    /**
+     * Compact representation of alignment
+     * @return CigarArray
+     */
+    public CigarArray getCompactAlignment();
 }