sequences are private in SequenceGroup

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

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 7fe4627..dbf3c35 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
@@ -154,25 +161,7 @@ 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
@@ -225,11 +214,6 @@ public interface AlignmentI
      */\r
     public void addAnnotation(AlignmentAnnotation aa);\r
 \r
-    /**\r
-     * Adds a new AlignmentAnnotation to this alignment,\r
-     *  associated to Sequence starting at sequence index\r
-     */\r
-    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);\r
 \r
     public void setAnnotationIndex(AlignmentAnnotation aa, int index);\r
 \r