X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=dbf3c3595d00b79e08c4b35135b8b3a020fbba68;hb=8b875ed4be8113683a34f4d4df36b3a6bb1c556e;hp=10ea1542cd7bae2cbe582fe61eeb036dfe1f92f1;hpb=81bf67e64fade340738792bfbcd8b3a3efd3a010;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 10ea154..dbf3c35 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -61,6 +61,13 @@ public interface AlignmentI
     public Vector getSequences();
 
     /**
+     * Gets sequences as a SequenceI[]
+     *
+     * @return All sequences in alignment.
+     */
+    public SequenceI [] getSequencesArray();
+
+    /**
      * Find a specific sequence in this alignment.
      *
      * @param i Index of required sequence.
@@ -154,25 +161,7 @@ public interface AlignmentI
      */
     public void removeGaps();
 
-    /**
-     * Removes redundant sequences from alignment.
-     *
-     * @param threshold Remove all sequences above the given threshold.
-     * @param sel Set of sequences which will have redundant sequences removed from.
-     *
-     * @return All sequences below redundancy threshold.
-     */
-    public Vector removeRedundancy(float threshold, Vector sel);
 
-    /**
-     * 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.
@@ -225,11 +214,6 @@ public interface AlignmentI
      */
     public void addAnnotation(AlignmentAnnotation aa);
 
-    /**
-     * Adds a new AlignmentAnnotation to this alignment,
-     *  associated to Sequence starting at sequence index
-     */
-    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef);
 
     public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
@@ -292,7 +276,8 @@ public interface AlignmentI
      */
     public boolean padGaps();
 
-     public void adjustSequenceAnnotations();
+    public void adjustSequenceAnnotations();
 
+    public HiddenSequences getHiddenSequences();
 
 }