elementAt instead of get for 1.1 compatibility

[jalview.git] / src / jalview / datamodel / AlignmentI.java

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index ebfb0ce..06e93d7 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -61,6 +61,13 @@ public interface AlignmentI
     public Vector getSequences();\r
 \r
     /**\r
+     * Gets sequences as a SequenceI[]\r
+     *\r
+     * @return All sequences in alignment.\r
+     */\r
+    public SequenceI [] getSequencesArray();\r
+\r
+    /**\r
      * Find a specific sequence in this alignment.\r
      *\r
      * @param i Index of required sequence.\r
@@ -104,17 +111,8 @@ public interface AlignmentI
      * @param start Start index of columns to delete.\r
      * @param end End index to columns to delete.\r
      */\r
-    public void deleteColumns(int start, int end);\r
+    public void deleteColumns(SequenceI seqs [], int start, int end);\r
 \r
-    /**\r
-     * Deletes all residues in every sequence of alignment within given columns.\r
-     *\r
-     * @param seq1 Index of first sequence to delete columns from.\r
-     * @param seq2 Index of last sequence to delete columns from.\r
-     * @param start Start index of columns to delete.\r
-     * @param end End index of columns to delete.\r
-     */\r
-    public void deleteColumns(int seq1, int seq2, int start, int end);\r
 \r
     /**\r
      * Finds sequence in alignment using sequence name as query.\r
@@ -154,25 +152,7 @@ public interface AlignmentI
      */\r
     public void removeGaps();\r
 \r
-    /**\r
-     * Removes redundant sequences from alignment.\r
-     *\r
-     * @param threshold Remove all sequences above the given threshold.\r
-     * @param sel Set of sequences which will have redundant sequences removed from.\r
-     *\r
-     * @return All sequences below redundancy threshold.\r
-     */\r
-    public Vector removeRedundancy(float threshold, Vector sel);\r
 \r
-    /**\r
-     * Finds group that sequence at index i in alignment is part of.\r
-     *\r
-     * @param i Index in alignment.\r
-     *\r
-     * @return First group found for sequence at position i. WARNING :\r
-     * Sequences may be members of several groups. This method is incomplete.\r
-     */\r
-    public SequenceGroup findGroup(int i);\r
 \r
     /**\r
      * Finds group that given sequence is part of.\r
@@ -290,5 +270,9 @@ public interface AlignmentI
     public void adjustSequenceAnnotations();\r
 \r
     public HiddenSequences getHiddenSequences();\r
-\r
+    /**\r
+     * Compact representation of alignment\r
+     * @return CigarArray\r
+     */\r
+    public CigarArray getCompactAlignment();\r
 }\r