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 ebd95d9..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
@@ -219,39 +208,12 @@ public interface AlignmentI
      */\r
     public void deleteAllGroups();\r
 \r
-    /**\r
-     * Adds a super group. A SuperGroup is a group of groups.\r
-     *\r
-     * @param sg Adds a new SuperGroup to alignment\r
-     */\r
-    public void addSuperGroup(SuperGroup sg);\r
-\r
-    /**\r
-     * Removes SuperGroup from alignment.\r
-     *\r
-     * @param sg This SuperGroup will be deleted from alignment.\r
-     */\r
-    public void removeSuperGroup(SuperGroup sg);\r
-\r
-    /**\r
-     * Finds any SuperGroup that a given SequenceGroup may be part of.\r
-     *\r
-     * @param sg SequenceGroup to search for.\r
-     *\r
-     * @return SuperGroup that contains the given SequenceGroup.\r
-     */\r
-    public SuperGroup getSuperGroup(SequenceGroup sg);\r
 \r
     /**\r
      * Adds a new AlignmentAnnotation to this alignment\r
      */\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
@@ -314,7 +276,8 @@ public interface AlignmentI
      */\r
     public boolean padGaps();\r
 \r
-     public void adjustSequenceAnnotations();\r
+    public void adjustSequenceAnnotations();\r
 \r
+    public HiddenSequences getHiddenSequences();\r
 \r
 }\r