X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignmentI.java;h=dbf3c3595d00b79e08c4b35135b8b3a020fbba68;hb=521ce3c96d5977a9bd941894eda7a13dd09deea9;hp=69a5ac62b098c51d2cb45750d554bd587c523284;hpb=7e4c4ad887a30dc26496087b0150f4ac2fe355ec;p=jalview.git

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 69a5ac6..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.
@@ -219,39 +208,14 @@ public interface AlignmentI
      */
     public void deleteAllGroups();
 
-    /**
-     * Adds a super group. A SuperGroup is a group of groups.
-     *
-     * @param sg Adds a new SuperGroup to alignment
-     */
-    public void addSuperGroup(SuperGroup sg);
-
-    /**
-     * Removes SuperGroup from alignment.
-     *
-     * @param sg This SuperGroup will be deleted from alignment.
-     */
-    public void removeSuperGroup(SuperGroup sg);
-
-    /**
-     * Finds any SuperGroup that a given SequenceGroup may be part of.
-     *
-     * @param sg SequenceGroup to search for.
-     *
-     * @return SuperGroup that contains the given SequenceGroup.
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg);
 
     /**
      * Adds a new AlignmentAnnotation to this alignment
      */
     public void addAnnotation(AlignmentAnnotation aa);
 
-    /**
-     * Adds a new AlignmentAnnotation to this alignment,
-     *  associated to Sequence starting at sequence index
-     */
-    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index);
+
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index);
 
     /**
      * Deletes a specific AlignmentAnnotation from the alignment.
@@ -312,5 +276,8 @@ public interface AlignmentI
      */
     public boolean padGaps();
 
+    public void adjustSequenceAnnotations();
+
+    public HiddenSequences getHiddenSequences();
 
 }